Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100432 |
| Name | oriT_pNDM-1_Dok01  |
| Organism | Escherichia coli |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_018994 (48617..49167 [+], 551 nt) |
| oriT length | 551 nt |
| IRs (inverted repeats) | IR1: 62..70, 71..79 (AACCCTTTC..GACAGGGTT) IR2: 143..150, 154..161 (TGGCCTGC..GGAGGCCA) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 551 nt
>oriT_pNDM-1_Dok01
GAGCAGAGCTATGTGTGACAAGAAGTATAGAAATTACGAGGTAGCCATCATGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAAGGCTAATCAGGAGCCTGTGATTTACCCGATCATTGAAGAAGCTCTGCATCGCTACAGCCAGCTCGTGTTTCATGAGCAGAGAGAGAAATATGAAGACCCGGCCAGAATTGGGGCATTTCTGGAAACCCTGATCACCGAAACCTGCCGGGCGTTGGAAGTGCAAATTGTCGATAGTGGCGGTGATTCATGGTCTGTCGATTCAGGAGAGTCGTTCTCACTGTGGCTTTCTTCCCATCCAGGAGAACTATCCATTAACCCGCAGCCCCATGAGGATGAGACCTCTTTGCGTGGCTTGCTGTATGAGCTCATCACCTGTGAGAGCGTGAAAACTGTTTTAAGGAGAACCGACT
GAGCAGAGCTATGTGTGACAAGAAGTATAGAAATTACGAGGTAGCCATCATGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAAGGCTAATCAGGAGCCTGTGATTTACCCGATCATTGAAGAAGCTCTGCATCGCTACAGCCAGCTCGTGTTTCATGAGCAGAGAGAGAAATATGAAGACCCGGCCAGAATTGGGGCATTTCTGGAAACCCTGATCACCGAAACCTGCCGGGCGTTGGAAGTGCAAATTGTCGATAGTGGCGGTGATTCATGGTCTGTCGATTCAGGAGAGTCGTTCTCACTGTGGCTTTCTTCCCATCCAGGAGAACTATCCATTAACCCGCAGCCCCATGAGGATGAGACCTCTTTGCGTGGCTTGCTGTATGAGCTCATCACCTGTGAGAGCGTGAAAACTGTTTTAAGGAGAACCGACT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 503 | GenBank | YP_006939880 |
| Name | TraI_pNDM-1_Dok01 |
UniProt ID | C4NVS7 |
| Length | 990 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 990 a.a. Molecular weight: 109356.90 Da Isoelectric Point: 4.9395
>YP_006939880.1 type IV conjugative transfer system protein TraI (plasmid) [Escherichia coli]
MLKALNKLFGGRSGVIETAPSVRVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEVDDDQEEDVSALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGSTESSKPD
AGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPFDA
FSASAETASTDATNSEIPDVAMPGKQEKQPKQDFVPQEQNSLQGDDFPMFGSSDEPPSWAIEPLPMLTDA
PEQTTPAPAMPPTDKPNLHEKDAKTLLVEMLAGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVILY
PDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQDA
FELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKPSPEQKAKGKDSQPQQKEKKVDVTSPVEEPQRQ
PVQEKQNVARLPKREVQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSGVT
PQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKKRQ
GKLYLEVNET
MLKALNKLFGGRSGVIETAPSVRVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEVDDDQEEDVSALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGSTESSKPD
AGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPFDA
FSASAETASTDATNSEIPDVAMPGKQEKQPKQDFVPQEQNSLQGDDFPMFGSSDEPPSWAIEPLPMLTDA
PEQTTPAPAMPPTDKPNLHEKDAKTLLVEMLAGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVILY
PDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQDA
FELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKPSPEQKAKGKDSQPQQKEKKVDVTSPVEEPQRQ
PVQEKQNVARLPKREVQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSGVT
PQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKKRQ
GKLYLEVNET
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | C4NVS7 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 46751..55841
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| P3D63_RS00345 (NDM1Dok01_N0072) | 42782..43015 | - | 234 | WP_001191890 | hypothetical protein | - |
| P3D63_RS00350 (NDM1Dok01_N0073) | 42997..43614 | - | 618 | WP_001249395 | hypothetical protein | - |
| P3D63_RS00355 (NDM1Dok01_N0074) | 43782..46754 | + | 2973 | WP_001326173 | MobH family relaxase | - |
| P3D63_RS00360 (NDM1Dok01_N0075) | 46751..48616 | + | 1866 | WP_000178857 | conjugative transfer system coupling protein TraD | virb4 |
| P3D63_RS00365 (NDM1Dok01_N0076) | 48627..49211 | + | 585 | WP_000332868 | hypothetical protein | - |
| P3D63_RS00370 (NDM1Dok01_N0077) | 49168..49797 | + | 630 | WP_000743449 | DUF4400 domain-containing protein | tfc7 |
| P3D63_RS00375 (NDM1Dok01_N0078) | 49807..50253 | + | 447 | WP_000122507 | hypothetical protein | - |
| P3D63_RS00380 (NDM1Dok01_N0079) | 50263..50640 | + | 378 | WP_000869297 | hypothetical protein | - |
| P3D63_RS00385 (NDM1Dok01_N0080) | 50640..51302 | + | 663 | WP_001231464 | hypothetical protein | - |
| P3D63_RS00390 (NDM1Dok01_N0081) | 51483..51626 | + | 144 | WP_001275801 | hypothetical protein | - |
| P3D63_RS00395 (NDM1Dok01_N0082) | 51638..52003 | + | 366 | WP_001052530 | hypothetical protein | - |
| P3D63_RS00400 (NDM1Dok01_N0083) | 52148..52429 | + | 282 | WP_000805625 | type IV conjugative transfer system protein TraL | traL |
| P3D63_RS00405 (NDM1Dok01_N0084) | 52426..53052 | + | 627 | WP_001049717 | TraE/TraK family type IV conjugative transfer system protein | traE |
| P3D63_RS00410 (NDM1Dok01_N0085) | 53036..53953 | + | 918 | WP_000794249 | type-F conjugative transfer system secretin TraK | traK |
| P3D63_RS00415 (NDM1Dok01_N0086) | 53953..55266 | + | 1314 | WP_024131605 | TraB/VirB10 family protein | traB |
| P3D63_RS00420 (NDM1Dok01_N0087) | 55263..55841 | + | 579 | WP_000793435 | type IV conjugative transfer system lipoprotein TraV | traV |
| P3D63_RS00425 (NDM1Dok01_N0088) | 55845..56237 | + | 393 | WP_000479535 | TraA family conjugative transfer protein | - |
| P3D63_RS00430 (NDM1Dok01_N0089) | 56522..57694 | + | 1173 | Protein_86 | IS1380-like element ISEcp1 family transposase | - |
| P3D63_RS00435 (NDM1Dok01_N0090) | 57800..58987 | + | 1188 | WP_080399009 | IS4 family transposase | - |
| P3D63_RS00440 (NDM1Dok01_N0091) | 59442..60587 | + | 1146 | WP_015056382 | class C beta-lactamase CMY-4 | - |
Host bacterium
| ID | 893 | GenBank | NC_018994 |
| Plasmid name | pNDM-1_Dok01 | Incompatibility group | IncA/C2 |
| Plasmid size | 195560 bp | Coordinate of oriT [Strand] | 48617..49167 [+] |
| Host baterium | Escherichia coli |
Cargo genes
| Drug resistance gene | blaCMY-4, dfrA12, aadA2, qacE, sul1, armA, msr(E), mph(E), blaNDM-1, blaTEM-1A |
| Virulence gene | htpB |
| Metal resistance gene | merR |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |