Transposon
Name: Tn5501.3
Family: Tn3        Group: Tn3000
Evidence of Transposition: yes
 Host     

Host Organism:Uncultured Bacterium Molecular Source:plasmid pAKD4
Date of Isolation:2010

 Map     



 Terminal Inverted Repeats (IR)     

IRL (Length: 38 bp)GGGGTTCTAAGCCGGAACCGCCGAAAATTCCGTCAGCC
IRR (Length: 38 bp)GGGGTTCTAAGCCAGAACCGCCGAAATTTCCGTCATCC

 Sequence     
DNA SequenceLength  6344 
--------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

 Recombination Sites     

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

 ORFs     
ORF Summary
Gene Name Associated TE Coordinates Class Sub Class Orientation
cupin2 Tn5501.3 438-920 Passenger Gene Other -
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   +

ORF Details
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:  
MNTDPQQRRV APPFRAGYRQ RRTLGYSCSV ITSQAKLIFG VDMEMESRIF SVTEYIRPSD GEPIRSVVLE TKDSAVVVWH AHPGQEITAH VHPDGQDTWT
VISGEAEYYQ GGGKVAHLKA GDIAIAKPGQ VHGALNTSPV PFVFVSVVAS GNAGFALAEK

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:  
MDTRLFAFVG ADIGPWRIVR AETRVGEPLP EAKRLNVVSA SELQSETNAP WILRGITSNE RYVMRAEKNE IVAKQQGLAR PEATCGALIP IRKNAAWWEL
TQDERRSVFE QSKHVQIGLQ YLPAVARKLH HCRDLSENEP FDFLNWFEYA PIHEVEFNRL LSELRASEEW KYVDREVDIR LTQAQV

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:  
VRVVWTPEAQ QDRADVWDYI AADNPRAAAR MDEIFSDAAA RLIQHPMLGK PGKIPGTREL IPHESYRLVY QIDGETVWIL TLVHTARLWP PVRD

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:  
MSKQAVFTMK LEPELRAEFM AEAEAAHRPA SQVLRELMRE FVQRQRESRE YDEFLRRKVE AGRASMRAGL GRSNDEVEAE FAARRASVAS QA

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:  
MRVSSDSDRQ STNLQRDALL AVGVDARHLF EDHASGAKDD RAGLARALEF VRPGDVLVVW KLDRLGRSLS HLLAIVTSLK KKQVAFRSLT ENLDTTTPSG
EFLFQVFGAL AQYERALIQE RVVAGLAAAR KRGRIGGRPQ AITGEKLEAI VAALDGGMSK AAVCRNFGVK RTTLIETLAR VGWTGSRGAS SR

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
tnpA TnpA Tn5501.3 3030 3283-6312 +
Class:   Transposase
Transpoase Chemistry:   DDE
Protein Sequence:  
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

 References     

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