Transposon
Name: Tn5563a
Family: Tn3        Group: Tn3
Evidence of Transposition: yes
 Host     

Host Organism:Pseudomonas mendocina strain LM7
Place of Origin:Lubin, Poland Date of Isolation:2014
Other Geographic Information:black shale ore collected in Lubin copper mine

 Map     



 Terminal Inverted Repeats (IR)     


 Sequence     
DNA SequenceLength  6253 
--------10 --------20 --------30 --------40 --------50 --------60 --------70 --------80 --------90 -------100
GGGGTTTGGG GAGCAATGGA ACCAAAAACC AACGTAAGCC CTACCAACGC TTTTCGGTGT CTTCTTCCCA GGCGCCCATC TCGACAAAAC AGTTGCGCAT 100
GTCGGCCTCC TGGCTGATCT CGGTCAGCAG GTCATGCACG CTCTTGTCCA GCTCATCGTC GCTCCGATAC GGAATGGTCA ACTCATAGTG GCCGGCATCC 200
AGCCGCTTCA TGCCATAGGG CTCCAGGCAG TAGCGCTCAA TGTTCTCCGT GGCCCGCTTC CGGCCGCGCA CGAACTTGCT GTTATTCACC ACCGCGAGGC 300
GCAGGGTGAC GGTGGCCACC CGCTCGGCGG CGGGCGGCTC TGCCGGCGAC GCGGCCGAAG GCTGCTGGTC GCGTGACCTG GCGCTCTTCT GGTACGCGCC 400
GATCTCGACA CCACGGTGGC GCAGGTAGCT GTACAGCGTG CTCTTGGAGA TGTGCAGCTT CTCGCCGATC GCGCTGACGC TCAGGCGACC TTCGCGGTAG 500
AGGGTTTCGG CCGCCATGGC GGTGGCCTCA GCCTTGGCTG GCAGGCCCTT GGGACGGCCA CCGATCCGGC CACGCGCCCG TGCGGCCGAC AGACCCGCCT 600
GAGTCCGCTC GCGGATCAGC TCGCGCTCGA ACTCCGCCAG CGAGGCGAAC AGGTTGAACA CCAGGCGGCC TTGGGCGTGG GTGGTGTCGA TGGGGTCATT 700
CAGGCTCTGT AAGCCGACCT TGCGCTCTGC CAGCTCGCCG ACCAACTCGA CCAGGTGCTT GAGGGAACGC CCAAGGCGAT CCAGCTTCCA GATCACCACG 800
GCATCACCCG GCCGCACGTT GGCCAGCAGT TTGTCCAACT CCGGCCGGGC GCTTTTCGCG CCGCTGGCGA TGTCTTGGTA GATGCGTTCG CACCCGGCCT 900
GTTTCAGGGC ATCGACTTGT AGGTCGGCTT TCTGATCCCG AGTGCTCACT CGCGCATAAC CGATCTTCAT CAAAAGTACT GTTTACTCGA CTACGTTAGT 1000
AATAGTTGAA CTTTGATTAA GCGTACCAGT TATTTGAACC GTAGCGCGGG GAGCTTAACG AACCGAGCCA TTCCTCGATA GAGTTCGGCA AAACCTTCGT 1100
TTTGTCGAAC CATTGCATCG CCCTTTGTGA TTGGCGTATA AACACACAAA CACCTATTAG CGGAGAACGC TATGAATACC ATTCGCTGGA ATGTCGCCGT 1200
CTCGGCCGAC ACCGACCAGT CGCTTCGGAT GTTTCTGGCC AGCCAGGGCG GCGGCCGTAA GGGCGACCTG TCGCGCTTCA TCGAAGAAGC GGTACGGGCA 1300
CACATCCTGG AGCTGAGCGC TGAGCAGGCC AAGGCCGCTA ACGCCCATCT GAGTGAGGCA GAATTGACCA ACGCGGTTGA CGAAGCGCTC GACTGGGCAC 1400
GTAAGCGCTG ATGCGGGTCG TGTTGGATAC CAACATCCTG TTCAGCGCCC TGATCTCGCC ACATGGCGCG CCCGATGCGA TCTACCGTGC CTGGCGGGCG 1500
GCGCGTTTCG AGGTGGTGAC CTCGCGGATG CAACTCGATG AAATTCGTCG AGCCAGCCGC TATCCCAAGC TTCAGGCCAT CCTACAGCCC GCCAAGGTGG 1600
GCGCCATGAT CAATAACCTG CAACGGGCTG TGGTACTGGA GCGCCTGACC ATCGAGGTCG AAGCCGATGA TCCGGATGAC TCGTTTTTGC TGGCCATGGC 1700
CTTGGCGGGC GATGCGGACT ACCTGGTAAC CGGTGATCGC CGCGCCGGCC TGCTGCAACG CGGGCACATC GAACGCACGC GGATCGTCAC GCCCGCCGTG 1800
TTCTGCGTCG AGGTGCTGTG ATCAATGCCG GTCGGTTTTC TGACTCAAGA GCAACGCGAC GGTTTTGGCC GCTATGTTGA TTCGCCCAGC CGTGAAGAGC 1900
TGGAACGTTA CTTCCACCTG AGCGATGAAG ACCGTGAAGC CATCCAGGTG CTGCGGGGTA ACCATAACCG TCTGGGTTAT GCCGTTCTGC TGACCACCGT 2000
CCGCTTCGTT GGCGTTCTGC CGGACAAGCC CGCCGCCGTG CCGGTGGAAG TCCTGCAGGT GCTTTGCCGA CAACTGGCGA TTCCAGACCC CGACTGCCTC 2100
CAGCGCTATA GCGATCATCG CCGCTGGATA CATGCCACCG ATATTCAGAA CCGCTTTGGC TATCGTCATT TCACCGATCC GGGCATCGGC TTTCGCTTGA 2200
GCCGCTGGCT GTATGCCCTC TGCTGGACGG GCACCGACCG GCCGGGAGTG CTGTTTGAGC GAGCCACCTC GTGGCTGTTC ACACAGAAAG TCCTCCTGCC 2300
TGGTGTGTCT CAACTAGAGC GCTTTATCGC CCAGTTGCGC AGTCGGGTCG AAGAACGCCT CTGGTTTACG CTGGGCCGCA GCGTGACTGA GGAACAGCGA 2400
TTGCAACTGC AAGACTTGCT GACGGTGGCC GAAGGCAACC GCAGCTCCCG GCTGGATCAA TTGCGCTCCG GCCCGGTCAT GGTCAGTGGC CCCGCGTTGA 2500
TTCGGGCACT GCGCCGGCTC GATGACGTGC GCGGCATCGG CATCACCTTG CCGGCGGCGG CGCACATCCC TCCCAGCCGT ATCGCCGCCC TGGCCCGCTT 2600
CGCCAACACG GCCAAGGTCA CCGCGATTAA TCGGCTGCCG GCGTCGCGGC GGATGGCGAC ACTGGTGGCC TTCGCACTCT GCCTGGAGGC GACTGCGCAC 2700
GACGACGCAC TGGAAGTCCT GGAGGCCTTG CTGCGCGACC TGTTCAGCAA CGCGGAGAAG GCCGACAAGA AAGCCCGCAT GCGCAGCCTG AAAGACCTGG 2800
ATCGGTCGGC CGCGACGCTC GCCGCCGCGT GCAAGGTCGT GCTGGACAGC TCGATCAGCG ATGACAACGT GCGCGCCCGG CTGTTCAACG ACCTGCCGAG 2900
GACCACCCTG GAAAAGGCCC TGGAAGAGGT CAACGCGCTG ATCCGCCCGG TAGATGACGT CTATTTTCTT GCATTGGAAG CGCGCTACCG CAGCGTGCGC 3000
CGCTTCCTGC CCGACCTGCT CAAGCACATC CGCTTCGGCT TCAGCCCGGC CGGCAAGGGC GTGGCGGCTA GTCTGGAGTG GCTGCAACTG AACCTGCCGC 3100
GCCGGAAGCC AGAGGATGAC GCGCCGCAGG AGATCGTGGC CAAGGCTTGG CAGAAGCACA TCACCCGCGA AGATGGCTCC CTCGACATGG GTGCCTATGT 3200
GTTCTGCACG CTCGATGCGC TGCGCACGGC CCTGCGCCGC CGCGATGTCT TCGTCTCGCC CAGTTGGCGC TATGCCGACC CGCGCCTTGG CCTGCTCGAC 3300
GGTGCCGAAT GGCTGGCGGC GCGACCGATC ATCTGCCGGT CACTGGGCCT GACCATCGAC GCCAAAACCA CCCTGGACGC CTTGTCCGTC GAGCTGGATG 3400
CAACCTGGCT GGCAGTAGCC GCGCGCCTGC CCGACAACCC GGCGATTCAA CTGAGCGAGA ACACCGAGGG CAAGACCGAA CTGTCGCTCG GGGCGCTGGA 3500
CAAGCTGGAC GAGCCCTGCT CGTTGCTGCA ACTGCGGGCG GCCGTGTCTG ACCTGATGCC GCGTGTCGAT CTGCCGGAAA TCCTCTTGGA AATCGCCGCC 3600
CGCACTGGCT TTTCCGAGGC CTTCACCCAT GTCTCCGAAC GCAATGCACG CGCCGACAAC CTGGTCACCA GCCTCTGCGC GGTGCTGTTG GGCGGGGCCT 3700
GCAACACCGG CCTGGAGCCC TTGATCCGCA CCGACAACCC GGCGCTGCGC CGTGACCGGC TGTCCTGGGT CAGCCAGAAT TATATCCGCG ACGACACCCT 3800
GTCAGCGGCT AACGCCATCC TGGTCGGAGC GCAAAGCCAA CTGGAACTGG CCCAAGTCTG GGGTGGCGGC GAGGTCGCCT CCGCCGATGG CATGCGCTTC 3900
GTCGTACCGG TGCGCACCGT GCATGCCGGC CCCAATCCGA AGTATTTCGG CACCGGCCGG GGTGTCACCT GGTACAACCT GATTTCCGAC CAATTCTCCG 4000
GCCTCAACGC CATCACCGTG CCCGGCACGC TGCGCGACAG CCTGGTGTTG CTGGCGGTCG TGCTGGAACA GCAGACCGAG TTGCAGCCGA CGCAAATCAT 4100
GACCGACACC GGGGCCTACA GCGATGTGGT GTTCGGGCTC TTCCGCCTAC TTGGCTACCA CTTCAGTCCG CGGCTGGCCG ATGTCGGCGG TACCCGCTTC 4200
TGGCGCACGC GCCCGGACGC GGACTACGGC AAGCTCAACG GGCTGGCCCG CCAGTCGGTC AAACTCGACC TGATCGCCGA GCACTGGGAC GACCTGCTGC 4300
GCCTGGCCGG CTCGCTCAAA CTCGGCCGGG TGCCGGCGAC TGGCATCATG CGCACGCTGC AAACGGGAGA TAGACCCACC CGGCTGGCCC AGGCGCTGGC 4400
CGAATTCGGG CGGATCGAAA AGACTCTGCA CACGTTGACC TATATCGACG ACGAGTCCAA GCGCCGCGCC ACCCTGACCC AGTTGAACCG AGGCGAAGGC 4500
CGGCACAGCC TGGCCCGCGC CGTGTTCCAC GGCAAACGCG GCGAGCTCCG CCAGCGCTAC CGCGAAGGCC AGGAAGACCA GCTCGGTGCT CTGGGCCTGG 4600
TGGTGAACAT CATCGTGCTG TGGAACACCC TCTACATGAC GGCGGCCGTG GAACGGCTCA AGCAGCACGG CTATCCAGTG CTGGAAGAGG ATTTGGCCCG 4700
GCTATCGCCG CTGATCTACG AGCACATCAA CATGCTCGGG CGGTATTCCT TTGCGGTACC GGAAGAAGTT GCGCGCGGCG AGCTGCGGCC ACTGCGTAAT 4800
CCAGACGACG ACCTGTGATC CCCCTAAACG CTATGAGCAA CACCCAAGCT GCTGCTGGAT CGGCGGGCAC TTCACCGAGC CGAACGAACA GAAAACGCAG 4900
CAATCCCCTG GGTTGGGGCG CAGCAGCGCC TTGCAGTTGC TGCACTCGTA ATAGAACTGG CAGGCGTCCG TGGGCATGGT TTCCGGCTTG GCGAAGCCGC 5000
AGCGCGGGCA AGTCAGCACG GACTCAAGGA CAATGGCGCT CATCGTGACC TCACTTCTGC ACTGTGGAGG GGTATCCCGC GTTCGCGGTC GCCTCAGTCA 5100
GTGCCTCGGG CTGGGCCTTA TCGGGATCGT AGGTGACGGT CGCCGTCTTC TGGTCGAAAT TGACCTGGAC GTCACTCACG CCGGACACCT TCTCCAGCGA 5200
CTTCTTGACC GTGATCGGAC AGAGTCCGCA CGTCATGTTC TGCACGTCGA GCGTGACGGT TTTCGGGGGA GCCGCCAGCG CCACGAAGGG CAAGGCGAAA 5300
AGCACGGCGA TCAGCAGTTT GCGCATGGTT AATCTCCTTC AGTAGAACAG CGGGGCGAGC CACGGCACGG CCAATAGGCC GAGCAGCAGC ACGCTGACGA 5400
TCCAGAACAC GAGTCGCTGT CGCACGAGCG TGCGCGGATC GGCGCAGGGT GTACCTGGCG TACAAACCTG TGGCACCAGG TAGAGCTTGC GGAATGCCAA 5500
TCCCAGGAAC AGTAGAGTCA ACCCGATGAA GAGGGGGCGT AGTGGCTCCA TCATGGTCAG AGCGCCCACC CACGTACCGC CGACACCGAG TGCCAACAGC 5600
ACCAGTGGCC CGACACAGCA CACCGACGCA CCGATGGCGG TCAGCGAACT CGCGACCAGC GAGCCTTTCC CGGTGAGTTG CATCCCCATT CCCATCTCCT 5700
GAGCCTGATT GCCTAGGTGC TATTCTAAAC TCCGTACCAA AGTACGGAAT CAAGGAGAAA GTGATGGCCA CAGAGCTGAC CATTGGCAAG CTGGCAGACG 5800
CCGCCGGGGT GAACGTCGAG ACGATCCGCT ACTACCAGCG ACGCGGGCTG CTGGATGAAC CAGCTAAACC CTTGGGTGGC CATCGGCGCT ATCCGGTGGA 5900
CATGGTGAAG CGACTGCGTT TCATCAAGCG GGCTCAGGCG CTGGGTTTCA CGCTCTCGGA AGTCGGTGGA CTGCTGACGC TGGATGAGTC GTGCGCCTGT 6000
GCCGAAACGC GAGCACGGGC TGCACGCAAG CTCGCGTTGA TCGAGCAGAA GATGGCCGAC TTGGTCGTCA TGCAGCAACT GTTAGGCGAA CTGGTGCAGC 6100
AATGTGATGC GGGAGACGGC GGAACGATCT GCCCGATCAT CGAGGCACTG ATCAGAGAGT AATGCCTGGC GGGTGAGCTG GAGATCGGAA AGCCCCTTTA 6200
CGGTGGGATT CAGAGCTTAC GTTGGTTTTT GGTTCCATTG CTCCCCAAAC CCC

 Recombination Sites     

Name Coordinates Gene Sequence
res 975-1110 136 AGTACTGTTT ACTCGACTAC GTTAGTAATA GTTGAACTTT GATTAAGCGT ACCAGTTATT
TGAACCGTAG CGCGGGGAGC TTAACGAACC GAGCCATTCC TCGATAGAGT TCGGCAAAAC
CTTCGTTTTG TCGAAC
res_site_III 985-1026 42 ACTCGACTAC GTTAGTAATA GTTGAACTTT GATTAAGCGT AC
res_site_II 1029-1059 31 GTTATTTGAA CCGTAGCGCG GGGAGCTTAA C
res_site_I 1083-1110 28 GTTCGGCAAA ACCTTCGTTT TGTCGAAC

 ORFs     
ORF Summary
Gene Name Associated TE Coordinates Class Sub Class Orientation
tnpR Tn5563a 41-970 Accessory Gene Resolvase -
RHH_6 Tn5563a 1172-1411 Passenger Gene Antitoxin +
PIN_3 Tn5563a 1411-1821 Passenger Gene Toxin +
tnpA Tn5563a 1825-4818 Transposase   +
merP Tn5563a 5051-5326 Passenger Gene Heavy Metal Resistance -
merT Tn5563a 5339-5695 Passenger Gene Heavy Metal Resistance -
merR Tn5563a 5764-6162 Passenger Gene Heavy Metal Resistance +

ORF Details
Gene Name Protein Name Associated TE Gene Length Coordinates Strand
tnpR TnpR Tn5563a 930 41-970 -
Class:   Accessory Gene
Sub Class:   Resolvase
Transpoase Chemistry:   Serine
Sequence Family:  Serine Site-Specific Recombinase
Protein Sequence:  
MKIGYARVST RDQKADLQVD ALKQAGCERI YQDIASGAKS ARPELDKLLA NVRPGDAVVI WKLDRLGRSL KHLVELVGEL AERKVGLQSL NDPIDTTHAQ
GRLVFNLFAS LAEFERELIR ERTQAGLSAA RARGRIGGRP KGLPAKAEAT AMAAETLYRE GRLSVSAIGE KLHISKSTLY SYLRHRGVEI GAYQKSARSR
DQQPSAASPA EPPAAERVAT VTLRLAVVNN SKFVRGRKRA TENIERYCLE PYGMKRLDAG HYELTIPYRS DDELDKSVHD LLTEISQEAD MRNCFVEMGA
WEEDTEKRW

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
RHH_6 RHH_6 Tn5563a 240 1172-1411 +
Class:   Passenger Gene
Sub Class:   Antitoxin
Function:   antitoxin; binds to DNA(IPR031914)
Sequence Family:  RHH_6 (Pfam:PF16762)
Comment:   Pfam PF16762.4
Protein Sequence:  
MNTIRWNVAV SADTDQSLRM FLASQGGGRK GDLSRFIEEA VRAHILELSA EQAKAANAHL SEAELTNAVD EALDWARKR

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
PIN_3 PIN_3 Tn5563a 411 1411-1821 +
Class:   Passenger Gene
Sub Class:   Toxin
Function:   cleave single stranded RNA (Pfam:PF13470)
Target:   single stranded RNA
Sequence Family:  PIN_3 (Pfam:PF13470)
Protein Sequence:  
MRVVLDTNIL FSALISPHGA PDAIYRAWRA ARFEVVTSRM QLDEIRRASR YPKLQAILQP AKVGAMINNL QRAVVLERLT IEVEADDPDD SFLLAMALAG
DADYLVTGDR RAGLLQRGHI ERTRIVTPAV FCVEVL

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
tnpA TnpA Tn5563a 2994 1825-4818 +
Class:   Transposase
Transpoase Chemistry:   DDE
Protein Sequence:  
MPVGFLTQEQ RDGFGRYVDS PSREELERYF HLSDEDREAI QVLRGNHNRL GYAVLLTTVR FVGVLPDKPA AVPVEVLQVL CRQLAIPDPD CLQRYSDHRR
WIHATDIQNR FGYRHFTDPG IGFRLSRWLY ALCWTGTDRP GVLFERATSW LFTQKVLLPG VSQLERFIAQ LRSRVEERLW FTLGRSVTEE QRLQLQDLLT
VAEGNRSSRL DQLRSGPVMV SGPALIRALR RLDDVRGIGI TLPAAAHIPP SRIAALARFA NTAKVTAINR LPASRRMATL VAFALCLEAT AHDDALEVLE
ALLRDLFSNA EKADKKARMR SLKDLDRSAA TLAAACKVVL DSSISDDNVR ARLFNDLPRT TLEKALEEVN ALIRPVDDVY FLALEARYRS VRRFLPDLLK
HIRFGFSPAG KGVAASLEWL QLNLPRRKPE DDAPQEIVAK AWQKHITRED GSLDMGAYVF CTLDALRTAL RRRDVFVSPS WRYADPRLGL LDGAEWLAAR
PIICRSLGLT IDAKTTLDAL SVELDATWLA VAARLPDNPA IQLSENTEGK TELSLGALDK LDEPCSLLQL RAAVSDLMPR VDLPEILLEI AARTGFSEAF
THVSERNARA DNLVTSLCAV LLGGACNTGL EPLIRTDNPA LRRDRLSWVS QNYIRDDTLS AANAILVGAQ SQLELAQVWG GGEVASADGM RFVVPVRTVH
AGPNPKYFGT GRGVTWYNLI SDQFSGLNAI TVPGTLRDSL VLLAVVLEQQ TELQPTQIMT DTGAYSDVVF GLFRLLGYHF SPRLADVGGT RFWRTRPDAD
YGKLNGLARQ SVKLDLIAEH WDDLLRLAGS LKLGRVPATG IMRTLQTGDR PTRLAQALAE FGRIEKTLHT LTYIDDESKR RATLTQLNRG EGRHSLARAV
FHGKRGELRQ RYREGQEDQL GALGLVVNII VLWNTLYMTA AVERLKQHGY PVLEEDLARL SPLIYEHINM LGRYSFAVPE EVARGELRPL RNPDDDL

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
merP MerP Tn5563a 276 5051-5326 -
Class:   Passenger Gene
Sub Class:   Heavy Metal Resistance
Target:   Mercury
Comment:   periplasmic binding protein
Protein Sequence:  
MRKLLIAVLF ALPFVALAAP PKTVTLDVQN MTCGLCPITV KKSLEKVSGV SDVQVNFDQK TATVTYDPDK AQPEALTEAT ANAGYPSTVQ K

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
merT MerT Tn5563a 357 5339-5695 -
Class:   Passenger Gene
Sub Class:   Heavy Metal Resistance
Target:   Mercury
Comment:   transport protein
Protein Sequence:  
MGMGMQLTGK GSLVASSLTA IGASVCCVGP LVLLALGVGG TWVGALTMME PLRPLFIGLT LLFLGLAFRK LYLVPQVCTP GTPCADPRTL VRQRLVFWIV
SVLLLGLLAV PWLAPLFY

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
merR MerR Tn5563a 399 5764-6162 +
Class:   Passenger Gene
Sub Class:   Heavy Metal Resistance
Target:   Mercury
Comment:   regulatory protein
Protein Sequence:  
MATELTIGKL ADAAGVNVET IRYYQRRGLL DEPAKPLGGH RRYPVDMVKR LRFIKRAQAL GFTLSEVGGL LTLDESCACA ETRARAARKL ALIEQKMADL
VVMQQLLGEL VQQCDAGDGG TICPIIEALI RE

 References