Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100034 |
| Name | oriT_pV404  |
| Organism | Escherichia coli |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | LM651376 (42424..42506 [-], 83 nt) |
| oriT length | 83 nt |
| IRs (inverted repeats) | 8..bp: 6..13, 17..24 (GTCGGGGC..GCCCTGAC) 17..bp: 31..47, 54..70 (GTAATTGTAATAGCGTC..GACGGTATTACAATTAC) |
| Location of nic site | 78..79 |
| Conserved sequence flanking the nic site |
CATCCTG|T |
| Note | minimal oriT sequence |
oriT sequence
Download Length: 83 nt
>oriT_pV404
CGGGACAGGATGTGTAATTGTAATACCGTCACACGCGACGCTATTACAATTACCATCTGGTCAGGGCTTCGCCCCGACACCCC
CGGGACAGGATGTGTAATTGTAATACCGTCACACGCGACGCTATTACAATTACCATCTGGTCAGGGCTTCGCCCCGACACCCC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Reference
[1] Riccobono E et al. (2014) Complete sequence of pV404, a novel IncI1 plasmid harbouring blaCTX-M-14 in an original genetic context. Int J Antimicrob Agents. 44(4):374-6. [PMID:25178920]
Relaxase
| ID | 33 | GenBank | CDW92102 |
| Name | NikB_pV404 |
UniProt ID | A0A078BC53 |
| Length | 899 a.a. | PDB ID | |
| Note | NikB relaxase | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 103902.42 Da Isoelectric Point: 7.5153
>CDW92102.1 NikB (plasmid) [Escherichia coli]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRNRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMNGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVVIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRNRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMNGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVVIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A078BC53 |
Reference
[1] Riccobono E et al. (2014) Complete sequence of pV404, a novel IncI1 plasmid harbouring blaCTX-M-14 in an original genetic context. Int J Antimicrob Agents. 44(4):374-6. [PMID:25178920]
Auxiliary protein
| ID | 50 | GenBank | CDW92101 |
| Name | NikA_pV404 |
UniProt ID | C7SA35 |
| Length | 110 a.a. | PDB ID | _ |
| Note | NikA oriT-specific DNA binding protein | ||
Auxiliary protein sequence
Download Length: 110 a.a. Molecular weight: 12613.57 Da Isoelectric Point: 10.7463
>CDW92101.1 NikA (plasmid) [Escherichia coli]
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | C7SA35 |
T4CP
| ID | 33 | GenBank | CDW92107 |
| Name | TrbC_pV404 |
UniProt ID | A0A078BC56 |
| Length | 763 a.a. | PDB ID | _ |
| Note | TrbC transfer protein | ||
T4CP protein sequence
Download Length: 763 a.a. Molecular weight: 86953.16 Da Isoelectric Point: 6.7713
>CDW92107.1 TrbC (plasmid) [Escherichia coli]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRIAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRTERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRIAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRTERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A078BC56 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 51588..91559
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| Locus_52 | 46957..47334 | - | 378 | CDW92104 | endoribonuclease L-PSP | - |
| Locus_53 | 47331..48488 | - | 1158 | CDW92105 | hypothetical protein | - |
| Locus_54 | 48500..49162 | + | 663 | CDW92106 | DNA-binding protein | - |
| Locus_55 | 49304..51595 | - | 2292 | CDW92107 | TrbC | - |
| Locus_56 | 51588..52658 | - | 1071 | CDW92108 | TrbB | trbB |
| Locus_57 | 52677..53885 | - | 1209 | CDW92109 | TrbA | trbA |
| Locus_58 | 54119..54322 | + | 204 | CDW92110 | PndC | - |
| Locus_59 | 54177..54329 | + | 153 | CDW92111 | PndA | - |
| Locus_60 | 55493..56725 | - | 1233 | CDW92112 | TnpA | - |
| Locus_61 | 56963..57163 | - | 201 | CDW92113 | TnpB | - |
| Locus_62 | 57821..58483 | - | 663 | CDW92114 | ExcA | - |
| Locus_63 | 57821..58264 | - | 444 | CDW92115 | ExcB | - |
| Locus_64 | 58554..60791 | - | 2238 | CDW92116 | TraY | traY |
| Locus_65 | 60819..61403 | - | 585 | CDW92117 | TraX | - |
| Locus_66 | 61432..62634 | - | 1203 | CDW92118 | TraW | traW |
| Locus_67 | 62601..63215 | - | 615 | CDW92119 | TraV | traV |
| Locus_68 | 63215..66259 | - | 3045 | CDW92120 | TraU | traU |
| Locus_69 | 66349..67149 | - | 801 | CDW92121 | TraT | traT |
| Locus_70 | 67133..67321 | - | 189 | CDW92122 | TraS | - |
| Locus_71 | 67385..67789 | - | 405 | CDW92123 | TraR | traR |
| Locus_72 | 67840..68367 | - | 528 | CDW92124 | TraQ | traQ |
| Locus_73 | 68367..69071 | - | 705 | CDW92125 | TraP | traP |
| Locus_74 | 69071..70360 | - | 1290 | CDW92126 | TraO | traO |
| Locus_75 | 70363..71346 | - | 984 | CDW92127 | TraN | traN |
| Locus_76 | 71357..72049 | - | 693 | CDW92128 | TraM | traM |
| Locus_77 | 72046..72393 | - | 348 | CDW92129 | TraL | traL |
| Locus_78 | 72411..76178 | - | 3768 | CDW92130 | sogL | - |
| Locus_79 | 72411..74945 | - | 2535 | CDW92131 | SogS | - |
| Locus_80 | 76268..76819 | - | 552 | CDW92132 | Nuc | - |
| Locus_81 | 76834..77124 | - | 291 | CDW92133 | TraK | traK |
| Locus_82 | 77121..78269 | - | 1149 | CDW92134 | TraJ | virB11 |
| Locus_83 | 78266..79084 | - | 819 | CDW92135 | TraI | traI |
| Locus_84 | 79081..79539 | - | 459 | CDW92136 | TraH | - |
| Locus_85 | 79934..80518 | - | 585 | CDW92137 | TraG | - |
| Locus_86 | 80578..81780 | - | 1203 | CDW92138 | TraF | - |
| Locus_87 | 81866..82690 | - | 825 | CDW92139 | TraE | traE |
| Locus_88 | 82841..83995 | - | 1155 | CDW92140 | Rci | - |
| Locus_89 | 84060..84305 | + | 246 | CDW92141 | OrfB | - |
| Locus_90 | 84307..84558 | - | 252 | CDW92142 | OrfB' | - |
| Locus_91 | 84600..84887 | - | 288 | CDW92143 | OrfD' | - |
| Locus_92 | 84922..85173 | + | 252 | CDW92144 | OrfC | - |
| Locus_93 | 85170..85388 | - | 219 | CDW92145 | OrfC' | - |
| Locus_94 | 85423..85632 | + | 210 | CDW92146 | OrfA' | - |
| Locus_95 | 85629..87053 | - | 1425 | CDW92147 | PilVA | - |
| Locus_96 | 85629..85970 | - | 342 | CDW92148 | OrfA | - |
| Locus_97 | 87053..87709 | - | 657 | CDW92149 | PilU | - |
| Locus_98 | 87694..88254 | - | 561 | CDW92150 | PilT | virB1 |
| Locus_99 | 88264..88878 | - | 615 | CDW92151 | PilS | - |
| Locus_100 | 88896..89993 | - | 1098 | CDW92152 | PilR | - |
| Locus_101 | 90006..91559 | - | 1554 | CDW92153 | PilQ | virB11 |
| Locus_102 | 91570..92022 | - | 453 | CDW92154 | PilP | - |
| Locus_103 | 92009..93304 | - | 1296 | CDW92155 | PilO | - |
| Locus_104 | 93297..94979 | - | 1683 | CDW92156 | PilN | - |
| Locus_105 | 94993..95430 | - | 438 | CDW92157 | PilM | - |
| Locus_106 | 95430..96497 | - | 1068 | CDW92158 | PilL | - |
Host bacterium
| ID | 33 | GenBank | LM651376 |
| Plasmid name | pV404 | Incompatibility group | IncI1 |
| Plasmid size | 101631 bp | Coordinate of oriT [Strand] | 42424..42506 [-] |
| Host baterium | Escherichia coli |
Cargo genes
| Drug resistance gene | beta-lactamase gene blaCTX-M-14 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |