Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100627 |
| Name | oriT_pNDM-US  |
| Organism | Klebsiella pneumoniae strain ATCC BAA-2146 |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP006661 (62712..63262 [+], 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-US
GAGCAGAGCTATGTGTGACAAGAAGTATAGAAATTACGAGGTAGCCATCATGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAAGGCTAATCAGGAGCCTGTGATTTACCCGATCATTGAAGAAGCTCTGCATCGCTACAGCCAGCTCGTGTTTCATGAGCAGAGAGAGAAATATGAAGACCCGGCCAGAATTGGGGCATTTCTGGAAACCCTGATCACCGAAACCTGCCGGGCGTTGGAAGTGCAAATTGTCGATAGTGGCGGTGATTCATGGTCTGTCGATTCAGGAGAGTCGTTCTCACTGTGGCTTTCTTCCCATCCAGGAGAACTATCCATTAACCCGCAGCCCCATGAGGATGAGACCTCTTTGCGTGGCTTGCTGTATGAGCTCATCACCTGTGAGAGCGTGAAAACTGTTTTAAGGAGAACCGACT
GAGCAGAGCTATGTGTGACAAGAAGTATAGAAATTACGAGGTAGCCATCATGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAAGGCTAATCAGGAGCCTGTGATTTACCCGATCATTGAAGAAGCTCTGCATCGCTACAGCCAGCTCGTGTTTCATGAGCAGAGAGAGAAATATGAAGACCCGGCCAGAATTGGGGCATTTCTGGAAACCCTGATCACCGAAACCTGCCGGGCGTTGGAAGTGCAAATTGTCGATAGTGGCGGTGATTCATGGTCTGTCGATTCAGGAGAGTCGTTCTCACTGTGGCTTTCTTCCCATCCAGGAGAACTATCCATTAACCCGCAGCCCCATGAGGATGAGACCTCTTTGCGTGGCTTGCTGTATGAGCTCATCACCTGTGAGAGCGTGAAAACTGTTTTAAGGAGAACCGACT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 699 | GenBank | WP_001326173 |
| Name | TraI_pNDM-US |
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
>WP_001326173.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
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: 60846..69936
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| kpn2146_RS27900 | 56877..57110 | - | 234 | WP_001191890 | hypothetical protein | - |
| kpn2146_RS27905 (Kpn2146_5548) | 57092..57709 | - | 618 | WP_001249395 | hypothetical protein | - |
| kpn2146_RS27910 (Kpn2146_5549) | 57877..60849 | + | 2973 | WP_001326173 | MobH family relaxase | - |
| kpn2146_RS27915 (Kpn2146_5550) | 60846..62711 | + | 1866 | WP_000178857 | conjugative transfer system coupling protein TraD | virb4 |
| kpn2146_RS27920 (Kpn2146_5551) | 62761..63306 | + | 546 | WP_000228720 | hypothetical protein | - |
| kpn2146_RS27925 (Kpn2146_5552) | 63263..63892 | + | 630 | WP_000743449 | DUF4400 domain-containing protein | tfc7 |
| kpn2146_RS27930 (Kpn2146_6172) | 63902..64348 | + | 447 | WP_000122507 | hypothetical protein | - |
| kpn2146_RS27935 (Kpn2146_5553) | 64358..64735 | + | 378 | WP_000869297 | hypothetical protein | - |
| kpn2146_RS27940 (Kpn2146_6173) | 64735..65397 | + | 663 | WP_001231464 | hypothetical protein | - |
| kpn2146_RS33650 (Kpn2146_6174) | 65578..65721 | + | 144 | WP_001275801 | hypothetical protein | - |
| kpn2146_RS27945 (Kpn2146_5554) | 65733..66098 | + | 366 | WP_001052530 | hypothetical protein | - |
| kpn2146_RS27950 (Kpn2146_5555) | 66243..66524 | + | 282 | WP_000805625 | type IV conjugative transfer system protein TraL | traL |
| kpn2146_RS27955 (Kpn2146_5556) | 66521..67147 | + | 627 | WP_001049717 | TraE/TraK family type IV conjugative transfer system protein | traE |
| kpn2146_RS27960 (Kpn2146_5557) | 67131..68048 | + | 918 | WP_000794249 | type-F conjugative transfer system secretin TraK | traK |
| kpn2146_RS27965 (Kpn2146_5558) | 68048..69361 | + | 1314 | WP_024131605 | TraB/VirB10 family protein | traB |
| kpn2146_RS27970 (Kpn2146_5559) | 69358..69936 | + | 579 | WP_000793435 | type IV conjugative transfer system lipoprotein TraV | traV |
| kpn2146_RS27975 (Kpn2146_5560) | 69940..70332 | + | 393 | WP_000479535 | TraA family conjugative transfer protein | - |
| kpn2146_RS27980 (Kpn2146_5561) | 70617..71879 | + | 1263 | WP_000608644 | IS1380-like element ISEcp1 family transposase | - |
| kpn2146_RS27990 (Kpn2146_5562) | 72203..73348 | + | 1146 | WP_015058212 | class C beta-lactamase CMY-6 | - |
| kpn2146_RS27995 (Kpn2146_5563) | 73442..73975 | + | 534 | WP_001221666 | lipocalin family protein | - |
| kpn2146_RS28000 (Kpn2146_5564) | 73972..74289 | - | 318 | WP_000118520 | quaternary ammonium compound efflux SMR transporter SugE | - |
| kpn2146_RS34080 | 74546..74911 | + | 366 | Protein_100 | LuxR family transcriptional regulator | - |
Host bacterium
| ID | 1087 | GenBank | NZ_CP006661 |
| Plasmid name | pNDM-US | Incompatibility group | IncA/C2 |
| Plasmid size | 140825 bp | Coordinate of oriT [Strand] | 62712..63262 [+] |
| Host baterium | Klebsiella pneumoniae strain ATCC BAA-2146 |
Cargo genes
| Drug resistance gene | blaCMY-6, aac(6')-Ib, qacE, sul1, rmtC, blaNDM-1 |
| Virulence gene | htpB |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |