Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 119105 |
| Name | oriT_p201605743-3  |
| Organism | Shigella sonnei strain 201605743 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_OP038300 (83815..83903 [-], 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_p201605743-3
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 12066 | GenBank | WP_011264053 |
| Name | nikB_OVQ04_RS00005_p201605743-3 |
UniProt ID | A0A767TAZ8 |
| Length | 899 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 103882.34 Da Isoelectric Point: 7.4198
>WP_011264053.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A767TAZ8 |
Auxiliary protein
| ID | 6900 | GenBank | WP_063119516 |
| Name | WP_063119516_p201605743-3 |
UniProt ID | _ |
| Length | 110 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 110 a.a. Molecular weight: 12585.55 Da Isoelectric Point: 10.6897
>WP_063119516.1 MULTISPECIES: IncI1-type relaxosome accessory protein NikA [Enterobacteriaceae]
MSDSAVKKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG
MSDSAVKKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG
Protein domains
No domain identified.
Protein structure
No available structure.
T4CP
| ID | 14129 | GenBank | WP_011264051 |
| Name | trbC_OVQ04_RS00010_p201605743-3 |
UniProt ID | _ |
| Length | 763 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 763 a.a. Molecular weight: 86954.10 Da Isoelectric Point: 6.7713
>WP_011264051.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKNNRPDWDGMY
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKNNRPDWDGMY
Protein domains
No domain identified.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 4485..42802
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| OVQ04_RS00010 (p201605743-3__00002) | 2201..4492 | - | 2292 | WP_011264051 | F-type conjugative transfer protein TrbC | - |
| OVQ04_RS00015 (p201605743-3__00003) | 4485..5555 | - | 1071 | WP_000151590 | IncI1-type conjugal transfer protein TrbB | trbB |
| OVQ04_RS00020 (p201605743-3__00004) | 5574..6782 | - | 1209 | WP_107372241 | IncI1-type conjugal transfer protein TrbA | trbA |
| OVQ04_RS00025 (p201605743-3__00005) | 7089..7868 | - | 780 | WP_275450201 | protein FinQ | - |
| OVQ04_RS00030 (p201605743-3__00006) | 8495..8647 | + | 153 | WP_001387489 | Hok/Gef family protein | - |
| OVQ04_RS00035 (p201605743-3__00007) | 8719..8970 | - | 252 | WP_001291964 | hypothetical protein | - |
| OVQ04_RS00490 | 9471..9566 | + | 96 | WP_000609148 | DinQ-like type I toxin DqlB | - |
| OVQ04_RS00045 (p201605743-3__00009) | 9631..9807 | - | 177 | WP_001054898 | hypothetical protein | - |
| OVQ04_RS00050 (p201605743-3__00010) | 10173..10382 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| OVQ04_RS00055 (p201605743-3__00011) | 10454..11128 | - | 675 | WP_223866377 | plasmid IncI1-type surface exclusion protein ExcA | - |
| OVQ04_RS00060 (p201605743-3__00012) | 11178..13346 | - | 2169 | WP_001774191 | DotA/TraY family protein | traY |
| OVQ04_RS00065 (p201605743-3__00013) | 13443..14027 | - | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| OVQ04_RS00070 (p201605743-3__00014) | 14056..15258 | - | 1203 | WP_107372242 | IncI1-type conjugal transfer protein TraW | traW |
| OVQ04_RS00075 (p201605743-3__00015) | 15225..15839 | - | 615 | WP_000337395 | IncI1-type conjugal transfer protein TraV | traV |
| OVQ04_RS00080 (p201605743-3__00016) | 15839..18883 | - | 3045 | WP_107372243 | IncI1-type conjugal transfer protein TraU | traU |
| OVQ04_RS00085 (p201605743-3__00017) | 18973..19773 | - | 801 | WP_107372244 | IncI1-type conjugal transfer protein TraT | traT |
| OVQ04_RS00090 (p201605743-3__00018) | 19757..19945 | - | 189 | WP_001277253 | putative conjugal transfer protein TraS | - |
| OVQ04_RS00095 (p201605743-3__00019) | 20009..20413 | - | 405 | WP_000086965 | IncI1-type conjugal transfer protein TraR | traR |
| OVQ04_RS00100 (p201605743-3__00020) | 20464..20991 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| OVQ04_RS00105 (p201605743-3__00021) | 20991..21695 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| OVQ04_RS00110 (p201605743-3__00022) | 21695..22984 | - | 1290 | WP_001271994 | conjugal transfer protein TraO | traO |
| OVQ04_RS00115 (p201605743-3__00023) | 22987..23970 | - | 984 | WP_001191879 | IncI1-type conjugal transfer protein TraN | traN |
| OVQ04_RS00120 (p201605743-3__00024) | 23981..24673 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| OVQ04_RS00125 (p201605743-3__00025) | 24670..25017 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| OVQ04_RS00130 (p201605743-3__00026) | 25035..28799 | - | 3765 | WP_001141540 | LPD7 domain-containing protein | - |
| OVQ04_RS00135 (p201605743-3__00027) | 28887..29438 | - | 552 | WP_000014586 | phospholipase D family protein | - |
| OVQ04_RS00140 (p201605743-3__00028) | 29453..29743 | - | 291 | WP_001314267 | hypothetical protein | traK |
| OVQ04_RS00145 (p201605743-3__00029) | 29740..30888 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| OVQ04_RS00150 (p201605743-3__00030) | 30885..31703 | - | 819 | WP_097763371 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| OVQ04_RS00155 (p201605743-3__00031) | 31700..32158 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| OVQ04_RS00160 (p201605743-3__00032) | 32553..33137 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| OVQ04_RS00165 (p201605743-3__00033) | 33197..34399 | - | 1203 | WP_000976353 | conjugal transfer protein TraF | - |
| OVQ04_RS00170 (p201605743-3__00034) | 34485..35309 | - | 825 | WP_001545755 | conjugal transfer protein TraE | traE |
| OVQ04_RS00175 (p201605743-3__00035) | 35460..36614 | - | 1155 | WP_001139958 | tyrosine-type recombinase/integrase | - |
| OVQ04_RS00180 | 36598..37020 | + | 423 | WP_162847923 | prepilin, shufflon protein A | - |
| OVQ04_RS00185 (p201605743-3__00036) | 37017..38309 | - | 1293 | WP_001390622 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| OVQ04_RS00190 (p201605743-3__00037) | 38309..38965 | - | 657 | WP_001193549 | A24 family peptidase | - |
| OVQ04_RS00195 (p201605743-3__00038) | 38950..39510 | - | 561 | WP_000014005 | lytic transglycosylase domain-containing protein | virB1 |
| OVQ04_RS00200 (p201605743-3__00039) | 39520..40134 | - | 615 | WP_000908227 | type 4 pilus major pilin | - |
| OVQ04_RS00205 (p201605743-3__00040) | 40151..41236 | - | 1086 | WP_001208802 | type II secretion system F family protein | - |
| OVQ04_RS00210 (p201605743-3__00041) | 41249..42802 | - | 1554 | WP_001545756 | GspE/PulE family protein | virB11 |
| OVQ04_RS00215 (p201605743-3__00042) | 42813..43265 | - | 453 | WP_001247333 | type IV pilus biogenesis protein PilP | - |
| OVQ04_RS00220 (p201605743-3__00043) | 43252..44547 | - | 1296 | WP_016245572 | type 4b pilus protein PilO2 | - |
| OVQ04_RS00225 (p201605743-3__00044) | 44540..46222 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| OVQ04_RS00230 (p201605743-3__00045) | 46236..46673 | - | 438 | WP_001545758 | type IV pilus biogenesis protein PilM | - |
| OVQ04_RS00235 (p201605743-3__00046) | 46673..47740 | - | 1068 | WP_001545759 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 19537 | GenBank | NZ_OP038300 |
| Plasmid name | p201605743-3 | Incompatibility group | IncI1 |
| Plasmid size | 84796 bp | Coordinate of oriT [Strand] | 83815..83903 [-] |
| Host baterium | Shigella sonnei strain 201605743 |
Cargo genes
| Drug resistance gene | blaCTX-M-3 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrVA2 |