Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 102912 |
| Name | oriT_FDAARGOS_90|unnamed1  |
| Organism | Shigella sonnei strain FDAARGOS_90 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP014096 (29436..29524 [+], 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_FDAARGOS_90|unnamed1
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 2187 | GenBank | WP_001360283 |
| Name | nikB_AL477_RS00130_FDAARGOS_90|unnamed1 |
UniProt ID | A0A637A499 |
| Length | 899 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 104011.40 Da Isoelectric Point: 7.3426
>WP_001360283.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A637A499 |
Auxiliary protein
| ID | 890 | GenBank | WP_001283947 |
| Name | WP_001283947_FDAARGOS_90|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 | 1858 | GenBank | WP_077108717 |
| Name | trbC_AL477_RS00125_FDAARGOS_90|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: 86945.09 Da Isoelectric Point: 6.7713
>WP_077108717.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKTRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHLTGRPVNGFHHKKTNRPDWDGMY
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKTRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHLTGRPVNGFHHKKTNRPDWDGMY
Protein domains
No domain identified.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 195..24058
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| AL477_RS00010 (AL477_26160) | 195..485 | + | 291 | WP_001314267 | hypothetical protein | traK |
| AL477_RS00015 (AL477_00010) | 500..1051 | + | 552 | WP_000014586 | phospholipase D family protein | - |
| AL477_RS00020 (AL477_00015) | 1141..4905 | + | 3765 | WP_061066705 | LPD7 domain-containing protein | - |
| AL477_RS00025 (AL477_00020) | 4923..5270 | + | 348 | WP_001055900 | conjugal transfer protein | traL |
| AL477_RS00030 (AL477_00025) | 5267..5959 | + | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| AL477_RS00035 (AL477_00030) | 5970..6953 | + | 984 | WP_001191879 | IncI1-type conjugal transfer protein TraN | traN |
| AL477_RS00040 (AL477_00035) | 6956..8245 | + | 1290 | WP_001271994 | conjugal transfer protein TraO | traO |
| AL477_RS00045 (AL477_00040) | 8245..8949 | + | 705 | WP_061066706 | IncI1-type conjugal transfer protein TraP | traP |
| AL477_RS00050 (AL477_00045) | 8949..9476 | + | 528 | WP_061066707 | conjugal transfer protein TraQ | traQ |
| AL477_RS00055 (AL477_00050) | 9527..9931 | + | 405 | WP_061066708 | IncI1-type conjugal transfer protein TraR | traR |
| AL477_RS00060 (AL477_00055) | 9995..10183 | + | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| AL477_RS00065 (AL477_00060) | 10167..10967 | + | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| AL477_RS00070 (AL477_00065) | 11057..14101 | + | 3045 | WP_061066709 | IncI1-type conjugal transfer protein TraU | traU |
| AL477_RS00075 (AL477_00070) | 14101..14715 | + | 615 | WP_000337399 | IncI1-type conjugal transfer protein TraV | traV |
| AL477_RS00080 (AL477_00075) | 14682..15884 | + | 1203 | WP_001189156 | IncI1-type conjugal transfer protein TraW | traW |
| AL477_RS00085 (AL477_00080) | 15913..16497 | + | 585 | WP_001476649 | IncI1-type conjugal transfer protein TraX | - |
| AL477_RS00090 (AL477_00085) | 16594..18762 | + | 2169 | WP_000698357 | DotA/TraY family protein | traY |
| AL477_RS00095 (AL477_00090) | 18836..19486 | + | 651 | WP_001178506 | plasmid IncI1-type surface exclusion protein ExcA | - |
| AL477_RS00100 (AL477_00095) | 19558..19767 | - | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| AL477_RS25780 | 20159..20335 | + | 177 | WP_001054898 | hypothetical protein | - |
| AL477_RS26665 | 20400..20495 | - | 96 | WP_001303310 | DinQ-like type I toxin DqlB | - |
| AL477_RS00105 (AL477_00110) | 20994..21245 | + | 252 | WP_001291964 | hypothetical protein | - |
| AL477_RS00110 (AL477_00115) | 21317..21469 | - | 153 | WP_001331364 | Hok/Gef family protein | - |
| AL477_RS00115 (AL477_00120) | 21761..22969 | + | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| AL477_RS00120 (AL477_00125) | 22988..24058 | + | 1071 | WP_061066710 | IncI1-type conjugal transfer protein TrbB | trbB |
| AL477_RS00125 (AL477_00130) | 24051..26342 | + | 2292 | WP_077108717 | F-type conjugative transfer protein TrbC | - |
Host bacterium
| ID | 3355 | GenBank | NZ_CP014096 |
| Plasmid name | FDAARGOS_90|unnamed1 | Incompatibility group | IncI1 |
| Plasmid size | 82828 bp | Coordinate of oriT [Strand] | 29436..29524 [+] |
| Host baterium | Shigella sonnei strain FDAARGOS_90 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |