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Internal Transposable Elements | |
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Internal Repeats | |
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Name: Tn5501.3 |
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Family: Tn3 Group: Tn3000 |
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Evidence of Transposition: yes |
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Host |
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Host Organism: | Uncultured Bacterium | Molecular Source: | plasmid pAKD4 |
| | Date of Isolation: | 2010 |
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Map |
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Terminal Inverted Repeats (IR) |
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IRL (Length: 38 bp) | | GGGGTTCTAAGCCGGAACCGCCGAAAATTCCGTCAGCC |
IRR (Length: 38 bp) | | GGGGTTCTAAGCCAGAACCGCCGAAATTTCCGTCATCC |
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Sequence |
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--------10 --------20 --------30 --------40 --------50 --------60 --------70 --------80 --------90 -------100
GGGGTTCTAA GCCGGAACCG CCGAAAATTC CGTCAGCCGA TCAACGTGGC TTGTCCCGCG CCCGGTCGAT GGGGTAGACC CAACAGTCGT GTCACTAGCC 100
GCCATTTCGA TCACGGCAAT GCCAGCCGGA CGTCACGTCC AGATTGTTCC GGTCTGGATG AGGCCGACTG ACGTCTCGGA TGACGGGTGG CATACAACTG 200
CTGTGAGTCC TGCAGGGGGG CAGCTGCCTG ACCGGACGGC GAGCATCAGC CCATCTCATG TATTAGTCAT GTCAGCTTTG ACACTGCGCA CGCGACGGCA 300
CCCGACCCGT TGCAGACCCC CAGACATATG GAAAGCTGAC GCTCAACGTG GAGTTAGCCG GCGCGGCGCG GCTTCATCGC GCAGCGTCCG TGTTGATGGA 400
TGGGTTAGAA CTCTCTGGGG CACACATTTG AGAAAGACTA TTTTTCAGCC AACGCAAAAC CCGCGTTGCC AGATGCAACC ACTGAGACAA ATACAAACGG 500
CACTGGACTA GTATTTAGAG CGCCATGCAC TTGGCCAGGT TTTGCTATGG CAATATCTCC AGCCTTTAGA TGAGCGACTT TGCCGCCTCC TTGGTAATAC 600
TCAGCCTCTC CAGAGATAAC CGTCCAAGTA TCTTGGCCGT CCGGGTGAAC ATGAGCGGTT ATTTCTTGCC CAGGATGGGC ATGCCAAACA ACAACTGCTG 700
AGTCCTTGGT TTCCAGAACC ACTGAACGAA TTGGTTCGCC GTCAGACGGA CGAATATATT CTGTTACCGA AAATATTCTT GATTCCATTT CCATATCCAC 800
TCCAAAAATC AATTTGGCTT GAGAAGTTAT TACAGAACAA CTGTATCCGA GAGTTCTACG TTGCCGATAA CCGGCCCGAA ACGGCGGCGC AACGCGCCGC 900
TGTTGGGGGT CCGTGTTCAT CGGCGGGTTA GACCTGTGCT TGCGTAAGAC GAATATCGAC TTCTCGGTCG ACGTATTTCC ATTCCTCTGA CGCACGCAGT 1000
TCGGAAAGCA GCCTGTTGAA CTCAACCTCA TGAATTGGCG CGTATTCGAA CCAATTCAGA AAATCGAACG GTTCATTCTC TGAGAGGTCG CGGCAGTGGT 1100
GGAGCTTGCG CGCTACTGCA GGCAAATACT GAAGCCCGAT TTGGACGTGC TTCGACTGTT CGAAAACGCT CCGGCGTTCG TCTTGCGTGA GCTCCCACCA 1200
AGCTGCGTTC TTCCGGATCG GTATTAGCGC ACCGCACGTT GCTTCTGGGC GCGCCAGACC TTGCTGCTTC GCTACAATTT CATTCTTCTC TGCGCGCATG 1300
ACATATCGTT CATTGCTGGT TATTCCACGA AGTATCCAGG GTGCATTGGT TTCAGACTGC AACTCTGAAG CGGATACGAC GTTGAGCCTT TTGGCTTCAG 1400
GCAGGGGCTC GCCAACTCTC GTTTCGGCCC TGACAATCCG CCAAGGGCCA ATGTCTGCGC CGACGAAAGC AAATAATCGT GTATCCATTT CAATCTTTCA 1500
TGTGTGAATG TTTTAACTCT TGCAGCTTCG AAGAACCTAT CTGCCGATCC CGTGATTGTG CATCATCGCC TCCGCGCAAC TGCGACGACC GCCCGCAGCA 1600
ATCACATTGA ACTTTCGAAT CGAAACTGCT GAAGCGAACC TACGCGGACG TACGGCCGCA GTCTGTGCGC TGCCGGACGG AGCGCTGCCA ATTTGCGCCT 1700
ACTGGCAGGC TGTGAGTGCG CGGATGGGCC AGCGACCTCC CTTCATAGAG GGAGCGAAGC AGGTCAGAGA CACTATTGAA CGTCCGCTAC CGGGAAGATG 1800
CTTGACCGTC CGCAACTGGC CGCCTGCCGC CGACCGCGGT CTGGCTCGAA AGCAGTCTGT CAACGCGCCG TTTCATTGTT GCCATGATCA TCTCTTAATC 1900
GCGCACAGGC GGCCACAGGC GGGCAGTATG AACCAGCGTC AGTATCCACA CCGTTTCGCC GTCGATCTGA TACACCAGGC GATAGCTTTC GTGCGGGATC 2000
AACTCGCGGG TCCCGGGAAT CTTTCCCGGC TTGCCCAGCA TGGGGTGCTG GATCAAGCGG GCGGCCGCGT CGCTGAAAAT CTCATCCATC CGGGCCGCCG 2100
CGCGCGGATT GTCGGCTGCG ATGTAGTCCC ACACATCGGC ACGGTCTTGC TGCGCTTCGG GCGTCCAAAC AACCCTCACG CCTGGCTCGC CACACTGGCA 2200
CGCCGTGCGG CGAATTCGGC CTCAACTTCA TCGTTCGACC GCCCCAATCC AGCGCGCATC GAAGCCCGGC CGGCTTCGAC CTTGCGGCGC AGGAACTCGT 2300
CGTACTCGCG CGACTCGCGC TGGCGCTGAA CGAACTCGCG CATCAGCTCG CGCAGCACTT GCGACGCCGG GCGATGGGCC GCCTCGGCTT CGGCCATAAA 2400
CTCGGCGCGC AACTCAGGCT CCAGCTTCAT CGTGAAAACG GCTTGTTTTG ACATGATCGG GGCCTCCTGC CACTTGATAC TAACAAAGTA TATACGCCGT 2500
CATTACTAAG CGCTATTCAC AGAACGCTGC AAGGCGGGCG TGCGCTAGGC CAAGGCCTGT CGGAAAACAT TTGTTTTTCG ACAGGCCTTC AACGGTCCTC 2600
TGCACCAACC TCCGAGTGGC CGCAAAATTG TGCGGAAAAC TCTGTCGCCA GACGCTACCA TACGGAAACC TCGTCTTAAT GGTTTTCCGC TTATGTTGGT 2700
AGGTTACATG CGCGTGTCGT CGGACTCCGA CCGCCAGAGC ACGAACTTGC AGCGCGATGC GCTGCTCGCC GTCGGCGTCG ATGCGCGGCA TCTGTTCGAG 2800
GATCATGCTT CCGGCGCGAA GGACGACCGC GCGGGCCTGG CGCGGGCGCT CGAATTCGTT CGCCCTGGCG ACGTGTTGGT CGTGTGGAAG CTCGACCGGC 2900
TCGGCCGTTC GTTGTCGCAC TTGCTCGCCA TCGTGACCTC GCTCAAGAAA AAGCAGGTGG CGTTCCGCTC GCTGACGGAG AACCTGGATA CCACGACGCC 3000
CTCGGGCGAG TTTCTGTTCC AGGTGTTCGG CGCGCTCGCG CAGTACGAAC GCGCCTTGAT CCAGGAACGT GTCGTCGCCG GTCTGGCTGC CGCCCGCAAA 3100
CGCGGCCGGA TCGGCGGCCG GCCGCAGGCG ATCACCGGCG AGAAGCTGGA GGCCATCGTC GCTGCGCTCG ATGGCGGCAT GTCCAAGGCG GCGGTGTGCC 3200
GCAACTTCGG CGTCAAGCGA ACCACGCTGA TCGAGACCCT GGCACGGGTT GGTTGGACGG GCTCTCGTGG AGCGTCATCG CGATGACGAC CAAGAGCGAA 3300
CGATTGACCG TCCTGTCGGA CGCCGAGCAG GAAGCCCTGT ACGGCCTGCC GGACTTCGAC GACGCCCAGC GGCTGGAATA CTTGGCGTTG ACTGAAACCG 3400
AACTGGCGCT CGCCAGCAGC CGGCCTGGTC TCCATGCCCA GGTCTATTGC ATCTTGCAGA TCGGTTACTT CAAGGCCAAG CATGCCTTCT TCCGCTTCGA 3500
CTGGAGTGAG GTCGAGCACG ATTGCGCCTT CGTGCTGAGC CGCTACTTCC ACGGCGAGTC CTTCGAGCAC AAGCCAATCT CCAAGCACGA GCACTACACC 3600
CAGCGCGAGT GGATTGCCGA TCTGTTCGGC TACCGGCCGT GGGCGGCCGA GTTCCTGGCG CAGCTCGCGC AGCAGGCCGC GCAGACCGTG CGGCGCGACG 3700
TGATGCCGGG GTTCATCGCC GCCGAGCTGA TCGTCTGGCT AAACGAGCAC AAGATCATCC GGCCCGGCTA TACCACCCTG CAAGAGCTGG TGAGCGAAGC 3800
CCTGTCCGCC GAGCGTCGGC GGCTGGCTGG CCTGCTGTCG GAAGTGTTGG ACGAATCGGC CAAGGCCGCG CTGGGTCGGC TTCTAGTGCG TGACGACACC 3900
CTGTCGCAAT TGGCGGCGCT CAAGCAGGAC GCCAAGGACT TTGGCTGGCG TCAGATGGCC CGCGAACGCG AAAAGCGCGC CACGCTGGAG CCGCTGCACC 4000
GGATCGCCAA GGCGCTGCTG CCCAAGCTCG GCGTCTCGCA GCAGAATCTG CTGTACTACG CCAGCCTGGC GAACTTCTAC ACCGTCCACG ATCTACGCAA 4100
CCTGAAGGCC GATCAGACCT ACCTCTACCT GCTTTGCTAT GCCTGGGTGC GCTACCGGCA GCTTTCCGAC AACCTGGTCG ATGCGATGGC CTACCACATG 4200
AAGCAGTTGG AGGACGAAAG CAGTGCGGGC GCAAAGCAAT CCTTTGTCGC CGAGCAGGTG CGCCGTCAGC AAGACACACC GCAGGTCGGC CGCCTGCTGT 4300
CGCTTTACAT CGACGACAGC GTGCCCGATC CCACGCCGTT CGGCGATGTG CGCCAGCGCG CCTACAAAAT CATGCCCCGC GATACGCTGC AAACCACCGC 4400
GCAGCGCATG AGCGTGAAGC CGGTGAGCAA GCTGGCTTTG CACTGGCAGG CGGTGGACGG CCTGGCTGAG CGCATCCGCC GCCATCTTCG GCCGCTGTAT 4500
GTCGCGCTCG ACCTCGCTGG CACTGATCCG GGCAGCCCGT GGCTCGTGGC GCTGGCCTGG GCCAAGGACG TGTTCGCCAA ACAGCAGCGC CTATCGCAAC 4600
GGCCGCTCGC CGAATGTCCA GCGGCCACGC TGCCGAAACG CTTGCGACCG TACCTGCTGA CCTTCGATGC CGATGGCAAG CCGACGGACC TGCATGCCGA 4700
CCGCTACGAG TTCTGGCTGT ACCGCCAGGT CAGGAAGCGC TTCCAGTCGG GTGAACTCTA CCTCGACGAC AGCTTGCAGC ACCGGCATTT TTCCGACGAG 4800
CTGGTTTCGC TGGATGAGAA GGCCGCCGTG CTGGCGCAGA TCGACATCCC GTTCCTGCGG CAGCCACTCG ATGCCCAGCT CGATGCGCTC GCGACCGAGC 4900
TGCGCGCTCA GTGGCTGGCC TTCAACCGCG AGCTGAAGCA GGGCAAGCTG ACGCACCTAG AATACGACAA GGACACGCAG AAGCTGACAT GGCGCAAGCC 5000
CAAGGGCGAG AACCAGAAGG CGCGCGAGAA GGCGTTCTAC GAGCAACTGC CGTTCTGCGA CGTGGCCGAC GTGTTCCGCT TCGTCAACGG CCAGTGCCAG 5100
TTCCTGTCGG CGCTGACGCC TTTGCAGCCG CGCTATGCGA AGAAGGTCGC CGACGCCGAC AGCCTGATGG CGGTCATCAT CGCGCAGGCG ATGAACCACG 5200
GCAACCAGGT CATGGCACGC ACCAGCGACA TCCCGTACCA CGTGCTGGAG AGCGCCTACC AACAGTACCT GCGCCACGCA ACGCTGCACG CGGCCAACGA 5300
CTGCATCAGC AACGCCATCG CCGCGCTGCC GATCTTCCCG TACTACTCGT TCGACCTCGA TGCACTGTAC GGTGCCGTCG ATGGTCAGAA ATTCGGCGTC 5400
GAGCGGCCGA CCGTGAAAGC GCGCCACTCG CGCAAATACT TTGGGCGCGG CAAGGGCGTG GTCGCCTACA CGCTGCTGTG CAACCACGTG CCGCTCAACG 5500
GCTACCTGAT CGGCGCGCAC GATTACGAGG CCCATCACGT GTTCGACATC TGGTATCGCA ACACGTCGGA CATCGTGCCG ACCGCGATCA CCGGCGACAT 5600
GCACAGCGTC AACAAGGCCA ACTTCGCTAT CCTGCACTGG TTCGGCCTGC GTTTCGAGCC GCGCTTCACC GACCTTGGCG ATCAGTTGAA GGAACTCTAC 5700
AGTGCCGACG ATCCGGCGCT GTACGATCAG TGCCTGATCC GGCCGGCCGG GAGAATCGAC CGCGATCTCA TAGTCAGCGA GAAGCCGAAC CTCGACCAGA 5800
TTGTCGCCAC GCTCGGACTG AAGGAGATGA CGCAGGGCAC GCTGATCCGC AAGCTATGCA CCTACACCGC GCCGAACCCC ACGCGGCGCG CGGTGTTCGA 5900
GTTCGACAAG CTCATCCGCA GCATCTACAC GCTGCGCTAC CTGCGCGATC CGCAACTGGA GCGCAACGTT CACCGCTCAC AGAACCGCAT CGAGTCCTAT 6000
CACCAGCTAC GCTCAACCAT CGCCCAGGTC GGCGGCAAGA AGGAATTGAC CGGGCGCACC GACATCGAAA TTGAGATCAG CAACCAGTGC GCCAGGCTGA 6100
TCGCCAACGC GGTCATCTTC TACAACTCGG CCATCCTCTC GCGGCTGCTG ATGAAGTACG AGGCGAGCGG CAACGCCAAG GCGCACGCTC TCCTGACCCA 6200
GATATCGCCG GCGGCCTGGC GGCACATCCT GCTGAACGGG CATTACACCT TCCAGAGCGA CGGCAAGATG ATCGACCTGG ATGCGCTCGT GGCGGGGCTG 6300
GAGCTGGGAT GACGGAAATT TCGGCGGTTC TGGCTTAGAA CCCC
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Recombination Sites |
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Name |
Coordinates |
Gene |
Sequence |
res |
2555-2685 |
131 |
GCCTGTCGGA AAACATTTGT TTTTCGACAG GCCTTCAACG GTCCTCTGCA CCAACCTCCG AGTGGCCGCA AAATTGTGCG GAAAACTCTG TCGCCAGACG CTACCATACG GAAACCTCGT CTTAATGGTT T |
res_site_I |
2555-2583 |
29 |
GCCTGTCGGA AAACATTTGT TTTTCGACA |
res_site_II |
2617-2660 |
44 |
TGGCCGCAAA ATTGTGCGGA AAACTCTGTC GCCAGACGCT ACCA |
res_site_III |
2661-2685 |
25 |
TACGGAAACC TCGTCTTAAT GGTTT |
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ORFs |
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Gene Name |
Associated TE |
Coordinates |
Class |
Sub Class |
Orientation |
cupin2 |
Tn5501.3 |
438-920 |
Passenger Gene |
Other |
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chlorite dismutase |
Tn5501.3 |
928-1488 |
Passenger Gene |
Other |
- |
parE |
Tn5501.3 |
1895-2179 |
Passenger Gene |
Toxin |
- |
parD |
Tn5501.3 |
2176-2454 |
Passenger Gene |
Antitoxin |
- |
tnpR |
Tn5501.3 |
2708-3286 |
Accessory Gene |
Resolvase |
+ |
tnpA |
Tn5501.3 |
3283-6312 |
Transposase |
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+ |
Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
cupin2 |
Cupin2 |
Tn5501.3 |
483 |
438-920 |
- |
Class: | Passenger Gene |
Sub Class: | Other |
Protein Sequence:
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MNTDPQQRRV APPFRAGYRQ RRTLGYSCSV ITSQAKLIFG VDMEMESRIF SVTEYIRPSD GEPIRSVVLE TKDSAVVVWH AHPGQEITAH VHPDGQDTWT VISGEAEYYQ GGGKVAHLKA GDIAIAKPGQ VHGALNTSPV PFVFVSVVAS GNAGFALAEK
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Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
chlorite dismutase |
Chlorite dismutase |
Tn5501.3 |
561 |
928-1488 |
- |
Class: | Passenger Gene |
Sub Class: | Other |
Protein Sequence:
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MDTRLFAFVG ADIGPWRIVR AETRVGEPLP EAKRLNVVSA SELQSETNAP WILRGITSNE RYVMRAEKNE IVAKQQGLAR PEATCGALIP IRKNAAWWEL TQDERRSVFE QSKHVQIGLQ YLPAVARKLH HCRDLSENEP FDFLNWFEYA PIHEVEFNRL LSELRASEEW KYVDREVDIR LTQAQV
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Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
parE |
ParE |
Tn5501.3 |
285 |
1895-2179 |
- |
Class: | Passenger Gene |
Sub Class: | Toxin |
Target: | DNA gyrase |
Sequence Family: | ParE_toxin (Pfam:PF05016) |
Protein Sequence:
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VRVVWTPEAQ QDRADVWDYI AADNPRAAAR MDEIFSDAAA RLIQHPMLGK PGKIPGTREL IPHESYRLVY QIDGETVWIL TLVHTARLWP PVRD
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Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
parD |
ParD |
Tn5501.3 |
279 |
2176-2454 |
- |
Class: | Passenger Gene |
Sub Class: | Antitoxin |
Sequence Family: | parD (PDB:4Q2U) |
Comment: | RelB |
Protein Sequence:
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MSKQAVFTMK LEPELRAEFM AEAEAAHRPA SQVLRELMRE FVQRQRESRE YDEFLRRKVE AGRASMRAGL GRSNDEVEAE FAARRASVAS QA
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Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
tnpR |
TnpR |
Tn5501.3 |
579 |
2708-3286 |
+ |
Class: | Accessory Gene |
Sub Class: | Resolvase |
Transpoase Chemistry: | Serine |
Sequence Family: | Serine Site-Specific Recombinase |
Protein Sequence:
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MRVSSDSDRQ STNLQRDALL AVGVDARHLF EDHASGAKDD RAGLARALEF VRPGDVLVVW KLDRLGRSLS HLLAIVTSLK KKQVAFRSLT ENLDTTTPSG EFLFQVFGAL AQYERALIQE RVVAGLAAAR KRGRIGGRPQ AITGEKLEAI VAALDGGMSK AAVCRNFGVK RTTLIETLAR VGWTGSRGAS SR
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Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
tnpA |
TnpA |
Tn5501.3 |
3030 |
3283-6312 |
+ |
Class: | Transposase |
Transpoase Chemistry: | DDE |
Protein Sequence:
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MTTKSERLTV LSDAEQEALY GLPDFDDAQR LEYLALTETE LALASSRPGL HAQVYCILQI GYFKAKHAFF RFDWSEVEHD CAFVLSRYFH GESFEHKPIS KHEHYTQREW IADLFGYRPW AAEFLAQLAQ QAAQTVRRDV MPGFIAAELI VWLNEHKIIR PGYTTLQELV SEALSAERRR LAGLLSEVLD ESAKAALGRL LVRDDTLSQL AALKQDAKDF GWRQMARERE KRATLEPLHR IAKALLPKLG VSQQNLLYYA SLANFYTVHD LRNLKADQTY LYLLCYAWVR YRQLSDNLVD AMAYHMKQLE DESSAGAKQS FVAEQVRRQQ DTPQVGRLLS LYIDDSVPDP TPFGDVRQRA YKIMPRDTLQ TTAQRMSVKP VSKLALHWQA VDGLAERIRR HLRPLYVALD LAGTDPGSPW LVALAWAKDV FAKQQRLSQR PLAECPAATL PKRLRPYLLT FDADGKPTDL HADRYEFWLY RQVRKRFQSG ELYLDDSLQH RHFSDELVSL DEKAAVLAQI DIPFLRQPLD AQLDALATEL RAQWLAFNRE LKQGKLTHLE YDKDTQKLTW RKPKGENQKA REKAFYEQLP FCDVADVFRF VNGQCQFLSA LTPLQPRYAK KVADADSLMA VIIAQAMNHG NQVMARTSDI PYHVLESAYQ QYLRHATLHA ANDCISNAIA ALPIFPYYSF DLDALYGAVD GQKFGVERPT VKARHSRKYF GRGKGVVAYT LLCNHVPLNG YLIGAHDYEA HHVFDIWYRN TSDIVPTAIT GDMHSVNKAN FAILHWFGLR FEPRFTDLGD QLKELYSADD PALYDQCLIR PAGRIDRDLI VSEKPNLDQI VATLGLKEMT QGTLIRKLCT YTAPNPTRRA VFEFDKLIRS IYTLRYLRDP QLERNVHRSQ NRIESYHQLR STIAQVGGKK ELTGRTDIEI EISNQCARLI ANAVIFYNSA ILSRLLMKYE ASGNAKAHAL LTQISPAAWR HILLNGHYTF QSDGKMIDLD ALVAGLELG
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References |
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Sen D, Yano H, Suzuki H, Król JE, Rogers L, Brown CJ, Top EM. Comparative genomics of pAKD4, the prototype IncP-1delta plasmid with a complete backbone. Plasmid. 2010 Mar;63(2):98-107. doi: 10.1016/j.plasmid.2009.11.005. Epub 2009 Dec 16. PubMed ID: 20018208
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