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Recombination Sites | |
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| Name: Tn6330 |
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| Family: Compound Transposon Group: ISApl1 |
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| Evidence of Transposition: yes |
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| Host |
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| Host Organism: | Escherichia coli strain EHS30-1 | Molecular Source: | plasmid pEHS30-1 |
| Place of Origin: | China | Date of Isolation: | 2016 |
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| Map |
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| Terminal Inverted Repeats (IR) |
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| IRL (Length: 27 bp) |  | GCTGAATTTACAATCCAAGTGCAACAA |
| IRR (Length: 27 bp) | | CTTGAATTGTCAAACCAAGTGCAACGA |
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| Sequence |
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--------10 --------20 --------30 --------40 --------50 --------60 --------70 --------80 --------90 -------100
GTGCTGAATT TACAATCCAA GTGCAACAAA AAAAGAAGTA CTCATCAACT AGAATATAAT TTTGTTTCCA CACAAAAACC ATTTCCAAAT GATGAGTACT 100
TCCTACCGAC ATCTTACAAT AAACGAGCGA GAAAAGATAA TGATTTTACT CGCACAGGGC AAAAAACAAG CAGAAATTGC CAAAGCACTG GGACGTAGCT 200
CCAGCACCAT TTCTCGCGAG CTGAAACGAC ACGCTCTAGA AAGCTACAGT GCAACGAACG CACAAAACAG CTATTTGAAG CATCGTCAAA ATAGCAAAGC 300
ACAGCGCAAA TTAGAGCAGC CTGAATATTT CAATTTGGTG CAAGAAAAGT TTCTGACAGA AAACTGGTCG CCCGAACAAA TCAGCGCACG ATTAAAATTG 400
GAAAAATCTG AATTATCCAT TAGTTATTCA ACCATTTATC GTGGTATTTA TTCAGGGTTG TTTGATATAG GCGAACGCAA AGCCAGTCGC AAACTGCGCC 500
ACAAAGGCAA AACACGGCAT ACAAAAAATC ATCATGAAAA ACGTGGCAAA ATTCAGATAT CCAACCATTT GAACGACCGT CCCATTTCGG CGCAAAATCG 600
CAGTCGCTTT GGACATTGGG AAGCCGATAC CGTACTGGGT AAAGCGGGTG GAGCTTGTTT GCTGACGCTG ACGGAACGCA AAAGTCGTTT TGAGTTGGTG 700
AAGAAAATTC CTGCCAAAAA AGCCGAAGCA GTCCAAAAAG CCATGATTGA ATTGCTGGAT TCACATATAT TGCGGTCAAT TACGCCAGAC CGTGGTAAAG 800
AATTTGCCCA ACATCGTTTG GTAACAGAAG CACTGGGTGT AGAATTTTAC TTCCCCGAGC CGCATCAACC GTGGACACGG GGAACGAATG AAAATACAAA 900
TGGGTTACTT CGTGAATACT TTCCGAAGCA CCAAGACATC AATCAGTGGA GCGAAGTTGA TATTCAACAG GTGATCAATA AACTGAATTT ACGACCACGT 1000
AAATGTTTAG GTTGGAAAAC ACCTTATGAA GTTTACTTCA AAAAATCGTT GCACTTGGTT TGACAATTCA AGATACAAAT TATAAATACT CTCAAGTGTA 1100
TATTCAGTAT GGGATTGCGC AATGATTGCC TAATAAAATT TCTGAAATAT TTCTGTATCG CATAATTTTT TATATCAGAT AAATTGTACT GGATTTCTTA 1200
AAAAATTGCA GTATAATTGC CGCAATTATC CCACCGTTTA TTTTTTTAAT AGTTTCTCAT GATGCAGCAT ACTTCTGTGT GGTACCGACG CTCGGTCAGT 1300
CCGTTTGTTC TTGTGGCGAG TGTTGCCGTT TTCTTGACCG CGACCGCCAA TCTTACCTTT TTTGATAAAA TCAGCCAAAC CTATCCCATC GCGGACAATC 1400
TCGGCTTTGT GCTGACGATC GCTGTCGTGC TCTTTGGCGC GATGCTACTG ATCACCACGC TGTTATCATC GTATCGCTAT GTGCTAAAGC CTGTGTTGAT 1500
TTTGCTATTA ATCATGGGCG CGGTGACCAG TTATTTTACT GACACTTATG GCACGGTCTA TGATACGACC ATGCTCCAAA ATGCCCTACA GACCGACCAA 1600
GCCGAGACCA AGGATCTATT AAACGCAGCG TTTATCATGC GTATCATTGG TTTGGGTGTG CTACCAAGTT TGCTTGTGGC TTTTGTTAAG GTGGATTATC 1700
CGACTTGGGG CAAGGGTTTG ATGCGCCGAT TGGGCTTGAT CGTGGCAAGT CTTGCGCTGA TTTTACTGCC TGTGGTGGCG TTCAGCAGTC ATTATGCCAG 1800
TTTCTTTCGC GTGCATAAGC CGCTGCGTAG CTATGTCAAT CCGATCATGC CAATCTACTC GGTGGGTAAG CTTGCCAGTA TTGAGTATAA AAAAGCCAGT 1900
GCGCCAAAAG ATACCATTTA TCACGCCAAA GACGCGGTAC AAGCAACCAA GCCTGATATG CGTAAGCCAC GCCTAGTGGT GTTCGTCGTC GGTGAGACGG 2000
CACGCGCCGA TCATGTCAGC TTCAATGGCT ATGAGCGCGA TACTTTCCCA CAGCTTGCCA AGATCGATGG CGTGACCAAT TTTAGCAATG TCACATCGTG 2100
CGGCACATCG ACGGCGTATT CTGTGCCGTG TATGTTCAGC TATCTGGGCG CGGATGAGTA TGATGTCGAT ACCGCCAAAT ACCAAGAAAA TGTGCTGGAT 2200
ACGCTGGATC GCTTGGGCGT AAGTATCTTG TGGCGTGATA ATAATTCGGA CTCAAAAGGC GTGATGGATA AGCTGCCAAA AGCGCAATTT GCCGATTATA 2300
AATCCGCGAC CAACAACGCC ATCTGCAACA CCAATCCTTA TAACGAATGC CGCGATGTCG GTATGCTCGT TGGCTTAGAT GACTTTGTCG CTGCCAATAA 2400
CGGCAAAGAT ATGCTGATCA TGCTGCACCA AATGGGCAAT CACGGGCCTG CGTATTTTAA GCGATATGAT GAAAAGTTTG CCAAATTCAC GCCAGTGTGT 2500
GAAGGTAATG AGCTTGCCAA GTGCGAACAT CAGTCCTTGA TCAATGCTTA TGACAATGCC TTGCTTGCCA CCGATGATTT CATCGCTCAA AGTATCCAGT 2600
GGCTGCAGAC GCACAGCAAT GCCTATGATG TCTCAATGCT GTATGTCAGC GATCATGGCG AAAGTCTGGG TGAGAACGGT GTCTATCTAC ATGGTATGCC 2700
AAATGCCTTT GCACCAAAAG AACAGCGCAG TGTGCCTGCA TTTTTCTGGA CGGATAAGCA AACTGGCATC ACGCCAATGG CAACCGATAC CGTCCTGACC 2800
CATGACGCGA TCACGCCGAC ATTATTAAAG CTGTTTGATG TCACCGCGGA CAAAGTCAAA GACCGCACCG CATTCATCCG CTGATTTCTC CCTGTATTTT 2900
TTCCAAACCC ACCGCACACT CCATTCGTAT TATGGGCGGT GGGGTGGGGT TTGTTATGCC GTATTTATCA AATAAACGCC TACTTGCTGA GATGAGTATC 3000
GCTCTTGTCA TGGCGATCGT TGCCACGCTG ACCCTTGAGC ACAGTCAGAT TGATCTGATG GTCGCTGATT GGTTTTATCT GGGTATGGGG CATTGGATGG 3100
TTGCCAAGCA AGCTTTTTTG CCAGATTTGC TACTGTATTC TGGACTAAAA AAGCTGCTGA TGGCGATGCT GATCTACTTG CTGGTTGCGA CCATTTGCCG 3200
TGCTTATCAT GAGAAAAAGG GCAATGCTAT CACTGCCAAG TGGCTTGTCC CAGTGACAAA ATTTCGCGTG CGTGAGCTTG CGTATCTGGT GCTGACTTTG 3300
ATCCTAGTGC CGACAGTTGT CGCGTCATTG AAGGCATATA CTCATGTGGT CTGCCCTGTG CATTTGACGA TTTTTGATGG TACGCTGCCG TATTTGCCGA 3400
TGCTTGATAG TATGCGTAAC ACCATTCCTG ATAAGTGCTT TCCTGCGGCG CATGCCAGTA GCGGATTTGC GCTGTTTGCC TTTGCGTTTG CGCCAAGTTT 3500
GCGCCGCCGT CGTGGTGCGA TCATCATCGT GGTGATGGCA TTGGGCTGGG CGATGGGCTG CTATAAGATG ATTATTGGCG ATCATTTTTT GAGCCATACG 3600
GTGGTGTCGA TGATGCTTGC GTGGGCGATG TCGGCAGGGC TTGCGTGGGT GTTTTTTAAG AAGGGTGAAC AAGTTTAATC GGCTGAATTT ACAATCCAAG 3700
TGCAACAAAA AAAGAAGTAC TCATCAACTA GAATATAATT TTGTTTCCAC ACAAAAACCA CTTCCAAATG ATGAGTACTT CCTACCGACA TCTTACAATA 3800
AACGAGCGAG AAAAGATAAT GATTTTACTC GCACAGGGCA AAAAACAAGC AGAAATTGCC AAAGCACTGG GACGTAGCTC CAGCACCATT TCTCGCGAGC 3900
TGAAACGACA CGCTCTAGAA AGCTACAGTG CAACGAACGC ACAAAACAGC TATTTGAAGC ATCGTCAAAA TAGCAAAGCA CAGCGCAAAT TAGAGCAGCC 4000
TGAATATTTC AATTTGGTGC AAGAAAAGTT TCTGACAGAA AACTGGTCGC CCGAACAAAT CAGCGCACGA TTAAAATTGG AAAAATCTGA ATTATCCATT 4100
AGTTATTCAA CCATTTATCG TGGTATTTAT TCAGGGTTGT TTGATATAGG CGAACGCAAA GCCAGTCGCA AACTGCGCCA CAAAGGCAAA ACACGGCATA 4200
CAAAAAATCA TCATGAAAAA CGTGGCAAAA TTCAGATATC CAACCATTTG AACGACCGTC CCATTTCGGC GCAAAATCGC AGTCGCTTTG GACATTGGGA 4300
AGCCGATACC GTACTGGGTA AAGCGGGTGG AGCTTGTTTG CTGACGCTGA CGGAACGCAA AAGTCGTTTT GAGTTGGTGA AGAAAATTCC TGCCAAAAAA 4400
GCCGAAGCAG TCCAAAAAGC CATGATTGAA TTGCTGGATT CACATATATT GCGGTCAATT ACGCCAGACC GTGGTAAAGA ATTTGCCCAA CATCGTTTGG 4500
TAACAGAAGC ACTGGGTGTA GAATTTTACT TCCCCGAGCC GCATCAACCG TGGACACGGG GAACGAATGA AAATACAAAT GGGTTACTTC GTGAATACTT 4600
TCCGAAGCAC CAAGACATCA ATCAGTGGAG CGAAGTTGAT ATTCAACAGG TGATCAATAA ACTGAATTTA CGACCACGTA AATGTTTAGG TTGGAAAACA 4700
CCTTATGAAG TTTACTTCAA AAAATCGTTG CACTTGGTTT GACAATTCAA GGT
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| ORFs |
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| Gene Name |
Associated TE |
Coordinates |
Class |
Sub Class |
Orientation |
| tnpA |
ISApl1 |
89-1063 |
Transposase |
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+ |
| MCR-1.1 (ARO:3003689) |
Tn6330 |
1259-2884 |
Passenger Gene |
Antibiotic Resistance |
+ |
| pap2 |
Tn6330 |
2956-3678 |
Passenger Gene |
Other |
+ |
| tnpA |
ISApl1 |
3768-4742 |
Transposase |
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+ |
| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| tnpA |
TnpA |
ISApl1 |
975 |
89-1063 |
+ |
| Class: | Transposase |
| Transpoase Chemistry: | DDE |
Protein Sequence:
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MMSTSYRHLT INEREKIMIL LAQGKKQAEI AKALGRSSST ISRELKRHAL ESYSATNAQN SYLKHRQNSK AQRKLEQPEY FNLVQEKFLT ENWSPEQISA
RLKLEKSELS ISYSTIYRGI YSGLFDIGER KASRKLRHKG KTRHTKNHHE KRGKIQISNH LNDRPISAQN RSRFGHWEAD TVLGKAGGAC LLTLTERKSR
FELVKKIPAK KAEAVQKAMI ELLDSHILRS ITPDRGKEFA QHRLVTEALG VEFYFPEPHQ PWTRGTNENT NGLLREYFPK HQDINQWSEV DIQQVINKLN
LRPRKCLGWK TPYEVYFKKS LHLV
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| MCR-1.1 (ARO:3003689) |
MCR-1.1 |
Tn6330 |
1626 |
1259-2884 |
+ |
| Class: | Passenger Gene |
| Sub Class: | Antibiotic Resistance |
| Function: | antibiotic target alteration (ARO:0001001) |
| Target: | peptide antibiotic (ARO:3000053) |
| Sequence Family: | MCR phosphoethanolamine transferase (ARO:3004268) |
| Comment: | perfect match to reference sequence for ARO:3003689||colistin resistance |
Protein Sequence:
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MMQHTSVWYR RSVSPFVLVA SVAVFLTATA NLTFFDKISQ TYPIADNLGF VLTIAVVLFG AMLLITTLLS SYRYVLKPVL ILLLIMGAVT SYFTDTYGTV
YDTTMLQNAL QTDQAETKDL LNAAFIMRII GLGVLPSLLV AFVKVDYPTW GKGLMRRLGL IVASLALILL PVVAFSSHYA SFFRVHKPLR SYVNPIMPIY
SVGKLASIEY KKASAPKDTI YHAKDAVQAT KPDMRKPRLV VFVVGETARA DHVSFNGYER DTFPQLAKID GVTNFSNVTS CGTSTAYSVP CMFSYLGADE
YDVDTAKYQE NVLDTLDRLG VSILWRDNNS DSKGVMDKLP KAQFADYKSA TNNAICNTNP YNECRDVGML VGLDDFVAAN NGKDMLIMLH QMGNHGPAYF
KRYDEKFAKF TPVCEGNELA KCEHQSLINA YDNALLATDD FIAQSIQWLQ THSNAYDVSM LYVSDHGESL GENGVYLHGM PNAFAPKEQR SVPAFFWTDK
QTGITPMATD TVLTHDAITP TLLKLFDVTA DKVKDRTAFI R
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| pap2 |
Pap2 |
Tn6330 |
723 |
2956-3678 |
+ |
| Class: | Passenger Gene |
| Sub Class: | Other |
| Sequence Family: | PAP2 (PF01569) |
| Comment: | truncated |
Protein Sequence:
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MPYLSNKRLL AEMSIALVMA IVATLTLEHS QIDLMVADWF YLGMGHWMVA KQAFLPDLLL YSGLKKLLMA MLIYLLVATI CRAYHEKKGN AITAKWLVPV
TKFRVRELAY LVLTLILVPT VVASLKAYTH VVCPVHLTIF DGTLPYLPML DSMRNTIPDK CFPAAHASSG FALFAFAFAP SLRRRRGAII IVVMALGWAM
GCYKMIIGDH FLSHTVVSMM LAWAMSAGLA WVFFKKGEQV
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| tnpA |
TnpA |
ISApl1 |
975 |
3768-4742 |
+ |
| Class: | Transposase |
| Transpoase Chemistry: | DDE |
Protein Sequence:
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MMSTSYRHLT INEREKIMIL LAQGKKQAEI AKALGRSSST ISRELKRHAL ESYSATNAQN SYLKHRQNSK AQRKLEQPEY FNLVQEKFLT ENWSPEQISA
RLKLEKSELS ISYSTIYRGI YSGLFDIGER KASRKLRHKG KTRHTKNHHE KRGKIQISNH LNDRPISAQN RSRFGHWEAD TVLGKAGGAC LLTLTERKSR
FELVKKIPAK KAEAVQKAMI ELLDSHILRS ITPDRGKEFA QHRLVTEALG VEFYFPEPHQ PWTRGTNENT NGLLREYFPK HQDINQWSEV DIQQVINKLN
LRPRKCLGWK TPYEVYFKKS LHLV
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| Internal Transposable Elements (TE) |
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| TnCentral Accession |
TE Name |
Type |
Coordinates |
Length |
| ISApl1-EF407820 |
ISApl1 |
Insertion Sequence |
3-1072 |
1070 |
| ISApl1-EF407820 |
ISApl1 |
Insertion Sequence |
3682-4751 |
1070 |
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| Internal Repeat Elements |
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| Name |
Associated Mobile Element |
Coordinates |
Sequence (Top Strand) |
| IRR |
ISApl1 |
1046-1072 |
AGCAACGTGA ACCAAACTGT TAAGTTC |
| IRL |
ISApl1 |
3682-3708 |
GCTGAATTTA CAATCCAAGT GCAACAA |
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| References |
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| 1. | Liu YY, Wang Y, Walsh TR, Yi LX, Zhang R, Spencer J, Doi Y, Tian G, Dong B, Huang X, Yu LF, Gu D, Ren H, Chen X, Lv L, He D, Zhou H, Liang Z, Liu JH, Shen J. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect Dis. 2016 Feb;16(2):161-8. doi: 10.1016/S1473-3099(15)00424-7. Epub 2015 Nov 19. PubMed ID: 26603172
| | | 2. | Li R, Xie M, Zhang J, Yang Z, Liu L, Liu X, Zheng Z, Chan EW, Chen S. Genetic characterization of mcr-1-bearing plasmids to depict molecular mechanisms underlying dissemination of the colistin resistance determinant. J Antimicrob Chemother. 2017 Feb;72(2):393-401. doi: 10.1093/jac/dkw411. Epub 2016 Sep 28. PubMed ID: 28073961
| | | 3. | Snesrud E, McGann P, Chandler M, ORCID: 0000-0002-0292-6662. The Birth and Demise of the ISApl1-mcr-1-ISApl1 Composite Transposon: the Vehicle for Transferable Colistin Resistance. mBio. 2018 Feb 13;9(1):e02381-17. doi: 10.1128/mBio.02381-17. PubMed ID: 29440577
| | | 4. | He YZ, Li XP, Miao YY, Lin J, Sun RY, Wang XP, Guo YY, Liao XP, Liu YH, Feng Y, Sun J. The ISApl1 (2) Dimer Circular Intermediate Participates in mcr-1 Transposition. Front Microbiol. 2019 Jan 22;10:15. doi: 10.3389/fmicb.2019.00015. eCollection 2019. PubMed ID: 30723461
| | | 5. | Li R, Chen K, Chan EW, Chen S. Characterization of the stability and dynamics of Tn6330 in an Escherichia coli strain by nanopore long reads. J Antimicrob Chemother. 2019 Jul 1;74(7):1807-1811. doi: 10.1093/jac/dkz117. PubMed ID: 30927434
| | | 6. | Liu X, Li R, Zheng Z, Chen K, Xie M, Chan EW, Geng S, Chen S. Molecular Characterization of Escherichia coli Isolates Carrying mcr-1, fosA3, and Extended-Spectrum-beta-Lactamase Genes from Food Samples in China. Antimicrob Agents Chemother. 2017 May 24;61(6). pii: AAC.00064-17. doi: 10.1128/AAC.00064-17. Print 2017 Jun. PubMed ID: 28373188
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