Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100479 |
| Name | oriT_pNDM-KN  |
| Organism | Klebsiella pneumoniae |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_019153 (11380..11930 [-], 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-KN
GAGCAGAGCTATGTGTGACAAGAAGTATAGAAATTACGAGGTAGCCATCATGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAAGGCTAATCAGGAGCCTGTGATTTACCCGATCATTGAAGAAGCTCTGCATCGCTACAGCCAGCTCGTGTTTCATGAGCAGAGAGAGAAATATGAAGACCCGGCCAGAATTGGGGCATTTCTGGAAACCCTGATCACCGAAACCTGCCGGGCGTTGGAAGTGCAAATTGTCGATAGTGGCGGTGATTCATGGTCTGTCGATTCAGGAGAGTCGTTCTCACTGTGGCTTTCTTCCCATCCAGGAGAACTATCCATTAACCCGCAGCCCCATGAGGATGAGACCTCTTTGCGTGGCTTGCTGTATGAGCTCATCACCTGTGAGAGCGTGAAAACTGTTTTAAGGAGAACCGACT
GAGCAGAGCTATGTGTGACAAGAAGTATAGAAATTACGAGGTAGCCATCATGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAAGGCTAATCAGGAGCCTGTGATTTACCCGATCATTGAAGAAGCTCTGCATCGCTACAGCCAGCTCGTGTTTCATGAGCAGAGAGAGAAATATGAAGACCCGGCCAGAATTGGGGCATTTCTGGAAACCCTGATCACCGAAACCTGCCGGGCGTTGGAAGTGCAAATTGTCGATAGTGGCGGTGATTCATGGTCTGTCGATTCAGGAGAGTCGTTCTCACTGTGGCTTTCTTCCCATCCAGGAGAACTATCCATTAACCCGCAGCCCCATGAGGATGAGACCTCTTTGCGTGGCTTGCTGTATGAGCTCATCACCTGTGAGAGCGTGAAAACTGTTTTAAGGAGAACCGACT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 550 | GenBank | YP_006958655 |
| Name | TraI_pNDM-KN |
UniProt ID | _ |
| 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_006958655.1 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
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 4707..13796
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HS808_RS00005 (D647_p3001) | 353..670 | + | 318 | WP_000118520 | quaternary ammonium compound efflux SMR transporter SugE | - |
| HS808_RS00010 (D647_p3002) | 667..1200 | - | 534 | WP_001221666 | lipocalin family protein | - |
| HS808_RS00015 (D647_p3003) | 1294..2439 | - | 1146 | WP_015058212 | class C beta-lactamase CMY-6 | - |
| HS808_RS00020 (D647_p3004) | 2764..4026 | - | 1263 | WP_000608644 | IS1380-like element ISEcp1 family transposase | - |
| HS808_RS00025 | 4311..4703 | - | 393 | WP_000479535 | TraA family conjugative transfer protein | - |
| HS808_RS00030 (D647_p3005) | 4707..5285 | - | 579 | WP_000793435 | type IV conjugative transfer system lipoprotein TraV | traV |
| HS808_RS00035 (D647_p3006) | 5282..6595 | - | 1314 | WP_024131605 | TraB/VirB10 family protein | traB |
| HS808_RS00040 (D647_p3007) | 6595..7512 | - | 918 | WP_000794249 | type-F conjugative transfer system secretin TraK | traK |
| HS808_RS00045 (D647_p3008) | 7496..8122 | - | 627 | WP_001049717 | TraE/TraK family type IV conjugative transfer system protein | traE |
| HS808_RS00050 (D647_p3009) | 8119..8400 | - | 282 | WP_000805625 | type IV conjugative transfer system protein TraL | traL |
| HS808_RS00055 (D647_p3010) | 8544..8909 | - | 366 | WP_001052530 | hypothetical protein | - |
| HS808_RS00060 | 8921..9064 | - | 144 | WP_001275801 | hypothetical protein | - |
| HS808_RS00065 (D647_p3011) | 9245..9907 | - | 663 | WP_001231464 | hypothetical protein | - |
| HS808_RS00070 | 9907..10284 | - | 378 | WP_000869297 | hypothetical protein | - |
| HS808_RS00075 (D647_p3012) | 10294..10740 | - | 447 | WP_000122507 | hypothetical protein | - |
| HS808_RS00080 (D647_p3013) | 10750..11379 | - | 630 | WP_000743449 | DUF4400 domain-containing protein | tfc7 |
| HS808_RS00085 (D647_p3014) | 11336..11920 | - | 585 | WP_000332868 | hypothetical protein | - |
| HS808_RS00090 (D647_p3015) | 11931..13796 | - | 1866 | WP_000178857 | conjugative transfer system coupling protein TraD | virb4 |
| HS808_RS00095 (D647_p3016) | 13793..16765 | - | 2973 | WP_001326173 | MobH family relaxase | - |
| HS808_RS00100 (D647_p3017) | 16933..17550 | + | 618 | WP_001249395 | hypothetical protein | - |
| HS808_RS00105 | 17532..17765 | + | 234 | WP_001191890 | hypothetical protein | - |
Host bacterium
| ID | 940 | GenBank | NC_019153 |
| Plasmid name | pNDM-KN | Incompatibility group | IncA/C2 |
| Plasmid size | 162746 bp | Coordinate of oriT [Strand] | 11380..11930 [-] |
| Host baterium | Klebsiella pneumoniae |
Cargo genes
| Drug resistance gene | blaCMY-6, blaNDM-1, rmtC, sul1, qacE, cmlA1, ant(3'')-Ia, ere(A), ARR-3 |
| Virulence gene | htpB |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |