Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100566 |
| Name | oriT_pKP1-NDM-1  |
| Organism | Klebsiella pneumoniae |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_023908 (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_pKP1-NDM-1
GAGCAGAGCTATGTGTGACAAGAAGTATAGAAATTACGAGGTAGCCATCATGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAAGGCTAATCAGGAGCCTGTGATTTACCCGATCATTGAAGAAGCTCTGCATCGCTACAGCCAGCTCGTGTTTCATGAGCAGAGAGAGAAATATGAAGACCCGGCCAGAATTGGGGCATTTCTGGAAACCCTGATCACCGAAACCTGCCGGGCGTTGGAAGTGCAAATTGTCGATAGTGGCGGTGATTCATGGTCTGTCGATTCAGGAGAGTCGTTCTCACTGTGGCTTTCTTCCCATCCAGGAGAACTATCCATTAACCCGCAGCCCCATGAGGATGAGACCTCTTTGCGTGGCTTGCTGTATGAGCTCATCACCTGTGAGAGCGTGAAAACTGTTTTAAGGAGAACCGACT
GAGCAGAGCTATGTGTGACAAGAAGTATAGAAATTACGAGGTAGCCATCATGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAAGGCTAATCAGGAGCCTGTGATTTACCCGATCATTGAAGAAGCTCTGCATCGCTACAGCCAGCTCGTGTTTCATGAGCAGAGAGAGAAATATGAAGACCCGGCCAGAATTGGGGCATTTCTGGAAACCCTGATCACCGAAACCTGCCGGGCGTTGGAAGTGCAAATTGTCGATAGTGGCGGTGATTCATGGTCTGTCGATTCAGGAGAGTCGTTCTCACTGTGGCTTTCTTCCCATCCAGGAGAACTATCCATTAACCCGCAGCCCCATGAGGATGAGACCTCTTTGCGTGGCTTGCTGTATGAGCTCATCACCTGTGAGAGCGTGAAAACTGTTTTAAGGAGAACCGACT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 638 | GenBank | YP_009023007 |
| Name | TraI_pKP1-NDM-1 |
UniProt ID | G9FJJ6 |
| 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_009023007.1 TraI (plasmid) [Klebsiella pneumoniae]
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 | G9FJJ6 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 46751..55841
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| H5I83_RS00345 | 42782..43015 | - | 234 | WP_001191890 | hypothetical protein | - |
| H5I83_RS00350 | 42997..43614 | - | 618 | WP_001249395 | hypothetical protein | - |
| H5I83_RS00355 (D647_p47045) | 43782..46754 | + | 2973 | WP_001326173 | MobH family relaxase | - |
| H5I83_RS00360 (D647_p47046) | 46751..48616 | + | 1866 | WP_000178857 | conjugative transfer system coupling protein TraD | virb4 |
| H5I83_RS00365 | 48627..49211 | + | 585 | WP_000332868 | hypothetical protein | - |
| H5I83_RS00370 (D647_p47048) | 49168..49797 | + | 630 | WP_000743449 | DUF4400 domain-containing protein | tfc7 |
| H5I83_RS00375 | 49807..50253 | + | 447 | WP_000122507 | hypothetical protein | - |
| H5I83_RS00380 | 50263..50640 | + | 378 | WP_000869297 | hypothetical protein | - |
| H5I83_RS00385 | 50640..51302 | + | 663 | WP_001231464 | hypothetical protein | - |
| H5I83_RS00390 | 51483..51626 | + | 144 | WP_001275801 | hypothetical protein | - |
| H5I83_RS00395 | 51626..52003 | + | 378 | WP_001326174 | hypothetical protein | - |
| H5I83_RS00400 (D647_p47052) | 52148..52429 | + | 282 | WP_000805625 | type IV conjugative transfer system protein TraL | traL |
| H5I83_RS00405 (D647_p47053) | 52426..53052 | + | 627 | WP_001049717 | TraE/TraK family type IV conjugative transfer system protein | traE |
| H5I83_RS00410 (D647_p47054) | 53036..53953 | + | 918 | WP_000794249 | type-F conjugative transfer system secretin TraK | traK |
| H5I83_RS00415 (D647_p47055) | 53953..55266 | + | 1314 | WP_024131605 | TraB/VirB10 family protein | traB |
| H5I83_RS00420 (D647_p47056) | 55263..55841 | + | 579 | WP_000793435 | type IV conjugative transfer system lipoprotein TraV | traV |
| H5I83_RS00425 | 55845..56237 | + | 393 | WP_000479535 | TraA family conjugative transfer protein | - |
| H5I83_RS00430 (D647_p47057) | 56522..57784 | + | 1263 | WP_000608644 | IS1380-like element ISEcp1 family transposase | - |
| H5I83_RS00435 (D647_p47058) | 58108..59253 | + | 1146 | WP_015058212 | class C beta-lactamase CMY-6 | - |
| H5I83_RS00440 (D647_p47059) | 59347..59880 | + | 534 | WP_001221666 | lipocalin family protein | - |
| H5I83_RS00445 (D647_p47060) | 59877..60194 | - | 318 | WP_000118520 | quaternary ammonium compound efflux SMR transporter SugE | - |
| H5I83_RS00450 | 60451..60816 | + | 366 | Protein_89 | LuxR family transcriptional regulator | - |
Host bacterium
| ID | 1026 | GenBank | NC_023908 |
| Plasmid name | pKP1-NDM-1 | Incompatibility group | IncA/C2 |
| Plasmid size | 137552 bp | Coordinate of oriT [Strand] | 48617..49167 [+] |
| Host baterium | Klebsiella pneumoniae |
Cargo genes
| Drug resistance gene | blaCMY-6, aac(6')-Ib, qacE, sul1, rmtC, blaNDM-1 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |