Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 120832 |
| Name | oriT_pSH11sh418-1  |
| Organism | Shigella sonnei strain sh11sh418 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_ON461899 (99837..99925 [-], 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_pSH11sh418-1
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 13141 | GenBank | WP_001306778 |
| Name | nikB_O1Z47_RS00565_pSH11sh418-1 |
UniProt ID | Q79VV7 |
| Length | 899 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 104010.41 Da Isoelectric Point: 7.4265
>WP_001306778.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q79VV7 |
Auxiliary protein
| ID | 7325 | GenBank | WP_001283947 |
| Name | WP_001283947_pSH11sh418-1 |
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 | 15420 | GenBank | WP_001289276 |
| Name | trbC_O1Z47_RS00570_pSH11sh418-1 |
UniProt ID | _ |
| Length | 763 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 763 a.a. Molecular weight: 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: 173..31904
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| O1Z47_RS00005 (pSH11sh418-1_00001) | 173..769 | - | 597 | WP_268737952 | conjugal transfer protein TraW | traW |
| O1Z47_RS00010 | 858..1454 | - | 597 | Protein_1 | IncI1-type conjugal transfer protein TraV | - |
| O1Z47_RS00015 | 1467..4506 | - | 3040 | Protein_2 | IncI1-type conjugal transfer protein TraU | - |
| O1Z47_RS00020 (pSH11sh418-1_00008) | 4595..5394 | - | 800 | Protein_3 | IncI1-type conjugal transfer protein TraT | - |
| O1Z47_RS00025 (pSH11sh418-1_00009) | 5378..5566 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| O1Z47_RS00030 | 5630..6032 | - | 403 | Protein_5 | IncI1-type conjugal transfer protein TraR | - |
| O1Z47_RS00035 (pSH11sh418-1_00012) | 6083..6610 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| O1Z47_RS00040 | 6610..7311 | - | 702 | Protein_7 | IncI1-type conjugal transfer protein TraP | - |
| O1Z47_RS00045 | 7311..8597 | - | 1287 | Protein_8 | conjugal transfer protein TraO | - |
| O1Z47_RS00050 | 8600..9581 | - | 982 | Protein_9 | IncI1-type conjugal transfer protein TraN | - |
| O1Z47_RS00055 (pSH11sh418-1_00018) | 9592..10284 | - | 693 | WP_000138550 | DotI/IcmL family type IV secretion protein | traM |
| O1Z47_RS00060 (pSH11sh418-1_00019) | 10281..10628 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| O1Z47_RS00065 | 10646..13317 | - | 2672 | Protein_12 | LPD7 domain-containing protein | - |
| O1Z47_RS00070 (pSH11sh418-1_00023) | 13377..14174 | - | 798 | WP_000544828 | IS21-like element IS21 family helper ATPase IstB | - |
| O1Z47_RS00075 (pSH11sh418-1_00024) | 14174..15346 | - | 1173 | WP_000952382 | IS21-like element IS21 family transposase | - |
| O1Z47_RS00080 (pSH11sh418-1_00025) | 15449..16543 | - | 1095 | Protein_15 | DUF5710 domain-containing protein | - |
| O1Z47_RS00085 (pSH11sh418-1_00026) | 16632..17183 | - | 552 | WP_000014583 | phospholipase D family protein | - |
| O1Z47_RS00090 (pSH11sh418-1_00027) | 17198..17488 | - | 291 | WP_001299214 | hypothetical protein | traK |
| O1Z47_RS00095 (pSH11sh418-1_00028) | 17485..18633 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| O1Z47_RS00100 (pSH11sh418-1_00029) | 18630..19448 | - | 819 | WP_000646098 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| O1Z47_RS00105 (pSH11sh418-1_00030) | 19445..19903 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| O1Z47_RS00110 (pSH11sh418-1_00031) | 20298..20882 | - | 585 | WP_268737953 | lipopolysaccharide core heptose(II)-phosphate phosphatase | - |
| O1Z47_RS00115 (pSH11sh418-1_00032) | 20942..22144 | - | 1203 | WP_000976351 | conjugal transfer protein TraF | - |
| O1Z47_RS00120 (pSH11sh418-1_00033) | 22229..23053 | - | 825 | WP_001238939 | conjugal transfer protein TraE | traE |
| O1Z47_RS00125 (pSH11sh418-1_00034) | 23204..24358 | - | 1155 | WP_001139957 | tyrosine-type recombinase/integrase | - |
| O1Z47_RS00130 | 24357..24710 | + | 354 | WP_001393368 | hypothetical protein | - |
| O1Z47_RS00135 (pSH11sh418-1_00035) | 24688..24969 | + | 282 | WP_244666015 | hypothetical protein | - |
| O1Z47_RS00140 (pSH11sh418-1_00037) | 26115..27398 | - | 1284 | Protein_27 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| O1Z47_RS00145 (pSH11sh418-1_00038) | 27398..28054 | - | 657 | WP_001193553 | prepilin peptidase | - |
| O1Z47_RS00150 (pSH11sh418-1_00039) | 28039..28599 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| O1Z47_RS00155 (pSH11sh418-1_00040) | 28609..29223 | - | 615 | WP_000959785 | type 4 pilus major pilin | - |
| O1Z47_RS00160 (pSH11sh418-1_00041) | 29241..30338 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| O1Z47_RS00165 (pSH11sh418-1_00042) | 30351..31904 | - | 1554 | WP_000362202 | GspE/PulE family protein | virB11 |
| O1Z47_RS00170 (pSH11sh418-1_00043) | 31915..32367 | - | 453 | WP_001247336 | type IV pilus biogenesis protein PilP | - |
| O1Z47_RS00175 (pSH11sh418-1_00044) | 32354..33649 | - | 1296 | WP_000752774 | type 4b pilus protein PilO2 | - |
| O1Z47_RS00180 (pSH11sh418-1_00045) | 33642..35324 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| O1Z47_RS00185 (pSH11sh418-1_00046) | 35338..35775 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| O1Z47_RS00190 (pSH11sh418-1_00047) | 35775..36841 | - | 1067 | Protein_37 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 21261 | GenBank | NZ_ON461899 |
| Plasmid name | pSH11sh418-1 | Incompatibility group | IncI1 |
| Plasmid size | 113792 bp | Coordinate of oriT [Strand] | 99837..99925 [-] |
| Host baterium | Shigella sonnei strain sh11sh418 |
Cargo genes
| Drug resistance gene | blaTEM-1B, aac(3)-IId, blaCTX-M-14 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |