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Internal Transposable Elements | |
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Internal Repeats | |
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Name: Tn5563a |
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Family: Tn3 Group: Tn3 |
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Evidence of Transposition: yes |
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Host |
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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 |
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Map |
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Terminal Inverted Repeats (IR) |
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Sequence |
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--------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
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Recombination Sites |
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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 |
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ORFs |
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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 |
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+ |
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 |
+ |
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:
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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
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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:
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MNTIRWNVAV SADTDQSLRM FLASQGGGRK GDLSRFIEEA VRAHILELSA EQAKAANAHL SEAELTNAVD EALDWARKR
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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:
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MRVVLDTNIL FSALISPHGA PDAIYRAWRA ARFEVVTSRM QLDEIRRASR YPKLQAILQP AKVGAMINNL QRAVVLERLT IEVEADDPDD SFLLAMALAG DADYLVTGDR RAGLLQRGHI ERTRIVTPAV FCVEVL
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Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
tnpA |
TnpA |
Tn5563a |
2994 |
1825-4818 |
+ |
Class: | Transposase |
Transpoase Chemistry: | DDE |
Protein Sequence:
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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
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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:
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MRKLLIAVLF ALPFVALAAP PKTVTLDVQN MTCGLCPITV KKSLEKVSGV SDVQVNFDQK TATVTYDPDK AQPEALTEAT ANAGYPSTVQ K
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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:
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MGMGMQLTGK GSLVASSLTA IGASVCCVGP LVLLALGVGG TWVGALTMME PLRPLFIGLT LLFLGLAFRK LYLVPQVCTP GTPCADPRTL VRQRLVFWIV SVLLLGLLAV PWLAPLFY
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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:
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MATELTIGKL ADAAGVNVET IRYYQRRGLL DEPAKPLGGH RRYPVDMVKR LRFIKRAQAL GFTLSEVGGL LTLDESCACA ETRARAARKL ALIEQKMADL VVMQQLLGEL VQQCDAGDGG TICPIIEALI RE
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References |
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Szuplewska M, Ludwiczak M, Lyzwa K, Czarnecki J, Bartosik D. Mobility and generation of mosaic non-autonomous transposons by Tn3-derived inverted-repeat miniature elements (TIMEs). PLoS One. 2014 Aug 14;9(8):e105010. doi: 10.1371/journal.pone.0105010. eCollection 2014. PubMed ID: 25121765
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