Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 120833 |
| Name | oriT_psh13D178-3  |
| Organism | Shigella sonnei strain sh13D178 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_ON461902 (58..146 [-], 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_psh13D178-3
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 13142 | GenBank | WP_053264317 |
| Name | nikB_O1Z48_RS00010_psh13D178-3 |
UniProt ID | A0A5T5LCD4 |
| Length | 899 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 103854.32 Da Isoelectric Point: 7.4198
>WP_053264317.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A5T5LCD4 |
Auxiliary protein
| ID | 7326 | GenBank | WP_001283947 |
| Name | WP_001283947_psh13D178-3 |
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 | 15421 | GenBank | WP_011264051 |
| Name | trbC_O1Z48_RS00015_psh13D178-3 |
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: 5525..49350
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| O1Z48_RS00015 (psh13D178-3_00003) | 3241..5532 | - | 2292 | WP_011264051 | F-type conjugative transfer protein TrbC | - |
| O1Z48_RS00020 (psh13D178-3_00004) | 5525..6595 | - | 1071 | WP_011264050 | IncI1-type conjugal transfer protein TrbB | trbB |
| O1Z48_RS00025 (psh13D178-3_00005) | 6614..7822 | - | 1209 | WP_011264049 | IncI1-type conjugal transfer protein TrbA | trbA |
| O1Z48_RS00030 (psh13D178-3_00006) | 8129..8911 | - | 783 | WP_023063753 | protein FinQ | - |
| O1Z48_RS00035 (psh13D178-3_00007) | 9107..9424 | + | 318 | WP_000118520 | quaternary ammonium compound efflux SMR transporter SugE | - |
| O1Z48_RS00040 (psh13D178-3_00008) | 9421..9954 | - | 534 | WP_001221666 | lipocalin family protein | - |
| O1Z48_RS00045 (psh13D178-3_00009) | 10048..11193 | - | 1146 | WP_000976514 | extended-spectrum class C beta-lactamase CMY-2 | - |
| O1Z48_RS00050 (psh13D178-3_00011) | 11517..12779 | - | 1263 | WP_000608644 | IS1380-like element ISEcp1 family transposase | - |
| O1Z48_RS00055 (psh13D178-3_00012) | 12932..13312 | - | 381 | WP_023518845 | hypothetical protein | - |
| O1Z48_RS00060 (psh13D178-3_00013) | 13627..13779 | + | 153 | WP_001387489 | Hok/Gef family protein | - |
| O1Z48_RS00065 (psh13D178-3_00014) | 13851..14102 | - | 252 | WP_001291964 | hypothetical protein | - |
| O1Z48_RS00435 | 14603..14698 | + | 96 | WP_000609148 | DinQ-like type I toxin DqlB | - |
| O1Z48_RS00075 | 14763..15047 | - | 285 | WP_001707309 | hypothetical protein | - |
| O1Z48_RS00080 (psh13D178-3_00017) | 15331..15540 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| O1Z48_RS00085 (psh13D178-3_00018) | 15612..16274 | - | 663 | WP_000644796 | plasmid IncI1-type surface exclusion protein ExcA | - |
| O1Z48_RS00090 (psh13D178-3_00019) | 16345..18513 | - | 2169 | WP_023518847 | DotA/TraY family protein | traY |
| O1Z48_RS00095 (psh13D178-3_00020) | 18610..19194 | - | 585 | WP_001746157 | IncI1-type conjugal transfer protein TraX | - |
| O1Z48_RS00100 (psh13D178-3_00021) | 19223..20425 | - | 1203 | WP_001189160 | IncI1-type conjugal transfer protein TraW | traW |
| O1Z48_RS00105 (psh13D178-3_00022) | 20392..21006 | - | 615 | WP_000337399 | IncI1-type conjugal transfer protein TraV | traV |
| O1Z48_RS00110 (psh13D178-3_00023) | 21006..24050 | - | 3045 | WP_023518848 | IncI1-type conjugal transfer protein TraU | traU |
| O1Z48_RS00115 (psh13D178-3_00024) | 24140..24940 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| O1Z48_RS00120 (psh13D178-3_00025) | 24924..25112 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| O1Z48_RS00125 (psh13D178-3_00026) | 25176..25580 | - | 405 | WP_000086965 | IncI1-type conjugal transfer protein TraR | traR |
| O1Z48_RS00130 (psh13D178-3_00027) | 25631..26158 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| O1Z48_RS00135 (psh13D178-3_00028) | 26158..26862 | - | 705 | WP_001493811 | IncI1-type conjugal transfer protein TraP | traP |
| O1Z48_RS00140 (psh13D178-3_00029) | 26862..28151 | - | 1290 | WP_011264042 | conjugal transfer protein TraO | traO |
| O1Z48_RS00145 (psh13D178-3_00030) | 28154..29137 | - | 984 | WP_001191879 | IncI1-type conjugal transfer protein TraN | traN |
| O1Z48_RS00150 (psh13D178-3_00031) | 29148..29840 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| O1Z48_RS00155 (psh13D178-3_00032) | 29837..30184 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| O1Z48_RS00160 (psh13D178-3_00033) | 30202..33969 | - | 3768 | WP_023518849 | LPD7 domain-containing protein | - |
| O1Z48_RS00165 (psh13D178-3_00034) | 34059..34610 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| O1Z48_RS00170 (psh13D178-3_00035) | 34625..34915 | - | 291 | WP_001299214 | hypothetical protein | traK |
| O1Z48_RS00175 (psh13D178-3_00036) | 34912..36060 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| O1Z48_RS00180 (psh13D178-3_00037) | 36057..36875 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| O1Z48_RS00185 (psh13D178-3_00038) | 36872..37330 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| O1Z48_RS00190 (psh13D178-3_00039) | 37725..38309 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| O1Z48_RS00195 (psh13D178-3_00040) | 38369..39571 | - | 1203 | WP_000976351 | conjugal transfer protein TraF | - |
| O1Z48_RS00200 (psh13D178-3_00041) | 39657..40481 | - | 825 | WP_023518851 | conjugal transfer protein TraE | traE |
| O1Z48_RS00205 (psh13D178-3_00042) | 40632..41786 | - | 1155 | WP_001139957 | tyrosine-type recombinase/integrase | - |
| O1Z48_RS00210 | 41770..42138 | + | 369 | WP_015059923 | hypothetical protein | - |
| O1Z48_RS00215 | 42961..43116 | - | 156 | WP_001302705 | hypothetical protein | - |
| O1Z48_RS00220 | 43307..43555 | + | 249 | WP_001349157 | hypothetical protein | - |
| O1Z48_RS00225 (psh13D178-3_00044) | 43552..44844 | - | 1293 | WP_001417545 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| O1Z48_RS00230 (psh13D178-3_00045) | 44844..45500 | - | 657 | WP_001193553 | prepilin peptidase | - |
| O1Z48_RS00235 (psh13D178-3_00046) | 45485..46045 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| O1Z48_RS00240 (psh13D178-3_00047) | 46055..46669 | - | 615 | WP_000959785 | type 4 pilus major pilin | - |
| O1Z48_RS00245 (psh13D178-3_00048) | 46687..47784 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| O1Z48_RS00250 (psh13D178-3_00049) | 47797..49350 | - | 1554 | WP_000362202 | GspE/PulE family protein | virB11 |
| O1Z48_RS00255 (psh13D178-3_00050) | 49361..49813 | - | 453 | WP_001247336 | type IV pilus biogenesis protein PilP | - |
| O1Z48_RS00260 (psh13D178-3_00051) | 49800..51095 | - | 1296 | WP_000752774 | type 4b pilus protein PilO2 | - |
| O1Z48_RS00265 (psh13D178-3_00052) | 51088..52770 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| O1Z48_RS00270 (psh13D178-3_00053) | 52784..53221 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| O1Z48_RS00275 (psh13D178-3_00054) | 53221..54288 | - | 1068 | WP_000742600 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 21262 | GenBank | NZ_ON461902 |
| Plasmid name | psh13D178-3 | Incompatibility group | IncI1 |
| Plasmid size | 79771 bp | Coordinate of oriT [Strand] | 58..146 [-] |
| Host baterium | Shigella sonnei strain sh13D178 |
Cargo genes
| Drug resistance gene | blaCMY-2 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrVA2 |