Transposon
Name: Tn5401
Family: Tn3        Group: Tn3
Evidence of Transposition: no
 Host     

Host Organism:Bacillus thuringiensis serovar morrisoni EG2158
Place of Origin:Kansas, U.S.A. Date of Isolation:1994
Other Geographic Information:soybean grain dust

 Map     



 Terminal Inverted Repeats (IR)     

IRL (Length: 53 bp)GGGGTATGTGTAGCAATGGAACAGAATCACGCAACAAGCATTAGCGGACATTA
IRR (Length: 53 bp)GGGGTATGTGTAGCAATGGAACAAAATCACGCAACAAGCATTAGCGGACATTA

 Sequence     
DNA SequenceLength  4837 
--------10 --------20 --------30 --------40 --------50 --------60 --------70 --------80 --------90 -------100
GGGGTATGTG TAGCAATGGA ACAGAATCAC GCAACAAGCA TTAGCGGACA TTATTCGCAC ACAAAAAAGG AAGGTTCTTC GATTCAGAAG ACCTTTCTTT 100
TAAAAATGCA TGTTTGCCTT ATTTATAGAT GTCACCACGA TTTCCAATTG CTTGTATGTA TATGACTTTC TCATCATGAT TTATTTCAAA TAAAATTCGA 200
AAGGTTCCAA TCCGTAATCG ATATAGTTCT GTGTAACCTT TCATACTTTT AATATCTCCT TCAGGAGGAA TCTTAAGAAG TCCCTTCAAT CCTTCTGCAA 300
TTCTTTTTTG AATCCCTTTT TCTTGCTTTG CAATAAATTT CACCGCGGAC TTATGGTAAA TCAATTTGTA GTCCGAATTC ACGTTTTGCG TCCTCCCCTG 400
ATACATATCC TTCTTCACTG TTTAACTGTT CTAACTCTTG TGTAGACAGC GGTTCATGAT CAGGATCTGC CATATCAATT TTTTCCCATT CTTTAGGTTT 500
TCTTCTTGAC CGTTGAACAA GAAATTCTAA AAAGTCAAAT GCTGCTTTTT CATCTTGTTG ATCCAGGTGA TCAATTAACC GATACAATTC ATCTTTACGA 600
ATAGCCATGT GTTACACCTA CTTTCGAGAT AGTTTTAAAT GTCCACTAAT TAATATTAGT GGACATGAAG TGTGGGAAAA TAAATGTTTG ATGTCCGCTA 700
ACATAATTGA TAAGATTAAA ATATCATGTC CGCTAATGTA AGTCAATAAA AGAGGAGGTA TTTATGCATT CCACTAAAAC AATTTCTATA CAAGCAACAT 800
CTTTGATTTC CGATTTTATT TCTAGCTTAT CTCAAGAAGG AGATTTGCAT ACAAAAACAC TAAAAGAATA TACGAGTGAT TTAAAAGATT TTGTATTTTG 900
GTTTGAAAAT GTGTGGGGAA AACATGCTGA GGATACTCTT TTTCATCCAA TAGAAGTTAC CGCTCGCACT ATTGCTCGAT ATCGAGGGCA TATGCAAGTT 1000
ACAAGATTAC TAAAACCTTC TACGATTAAC CGGCGCATTA ATTCAATCAA ACGTTATTTT GACTGGGCTA AGCAAAAAGG ACTGGTACAA ACAAATTATT 1100
CAAAATCAAT TAAGTTTGTA CCAACAGAAA AAACGAGTCC CAAACGCATG TCAGATAAAG AAGAAGCCGC TTTAATGCAT GCCGTTGAAA AATACGGCAC 1200
ACTACGTGAC AGGGCAATGA TTATTTTTAT GCTTCATACT GGCCTTCGTT CAATGGAAGT GTGTGATGTT CAAATAGAGG ATGTTATCAT GAGAAAAAGA 1300
GGCGGCTATG TTGTTGTTCG ATCTGGAAAA CGAAATAAAC AGAGGGAAGT GCCTTTGAAT AGTACAGCTC GTTGTGCACT AGAAGAACAT ATCAGATTAA 1400
GTGAGATTTC ACAGAGTTAT TTGTTTCCTT CTTCTAAAAC AGGAAAACGC CTACAAGAAA GAGCGATCCG CCATATTCTT CAGAAGTATA TTAGACTTGC 1500
AAAGTTAGAA GGATTTAGTG CCCATGATTT AAGGCATCGC TTTGGTTATG TGATGGCTGA ACGCACACCA TTACATCGTC TTGCACAAAT TATGGGACAC 1600
GATAACTTGA ATACCACGAT GATTTATGTA AGAGCTACAC AAGAAGATTT ACAGGGAGAA GTAGAAAAGA TTGCCTGGAA CTAAAGAATG CACATTATCC 1700
TACTCATTTG GTCATGTGAT ACAAAATAAG AATTGTAACA GGAGGAACAA GGGTTATGCC TGTAGATTTT TTAACACCTG AACAAGAAGA AAAATATGGT 1800
TGTTTTTGTG ACACTCCAAC ATCAGAGCAG TTAGCAAAAT ATTTTTGGTT AGATGATACA GACAAAGAAC TGATATGGAA TCGTCGTGGA GAGCATAATC 1900
AACTTGGTTT CGCTGTTCAA TTAGGAACCG TTAGGTTCTT AGGAACATTT TTATCTGATC CTACAAATGT ACCACAATCG GTTATTACAT ATATGGCAAA 2000
TCAACTTCAT CTAGATGCTC AAAGCTTTTC TCGTTATCGA AATAAACGAA GTCAGTGGGA TCAAATGCAA GAGATACGTT CTGTTTATGG ATATAAAAAC 2100
TTTACAGATA AATCAACACA TTGGCGATTC ATCAGATGGC TATATGCACG TGCTTGGCTA TATAATGAAC GGCCAAGTGT CTTATTTGAT TTAGCAACAG 2200
CACGATGTAT CGAACAAAAA ATTTTACTAC CTGGTGTATC TGTATTAACA AGGCTAGTAT CAACGGTTCG TGATCGTTCA GCAGAAAATA TATGGAAAAA 2300
GCTCTCTAGT CTTCCGGATA ATGTTCAGAA AAAACAATTA GAAAACCTTC TTCAGATAGA TCAAAAAACA AAGAAAACGT ATTTAGAGCG TCTAAGTAAT 2400
CCCCCTGTTC CGATTAGTGT TACGGGCATT AAGAATACGC TGATTCGTTT ACAAGAGCTT CGTCAATTGA ACACTGAAAA TTGGGATATG TCTAGAATTC 2500
CTTCGAAAAG ATTACAACAA TTCGCGCGTC ACACAGTCGC TGTTAGATCA CAAGCAATTG CTAGAATGCC CGATCAACGA CGTATGGCTA TGTTAGTTGC 2600
ATTTGCTAAA ATGTATACAC AAAGTGCTCA GGATGATGTC ATTGATATTT TTGATAGATA TTTAACAGAT TTATTTGCTA AGACATATCG AAAGGAACAA 2700
AAAGAACGTC TTCGTACAAT TAAGGATTTA GATAAGGCAG CGCGCCAATT ACGGGAAGCT TGTGTAATAT TATTAGAACA TACGGATCCT TCTGTCCATC 2800
CAAAAACGGC AGTGTTTGAA AAAATTTCAG AAAAGGATTT AATACAAGCT GTCCAAATTG TTGATTCACT CACCTATTCA CCAAATCAAA CACTAGCCTA 2900
TTCAGGATTG TTACAACATT ATGGCATAAT CCGAAAATTT CTTCCTTTAC TCATGGAAGA AATTGAATTA CAAGCAACGC CTGCTGGATT ACCCATCTTG 3000
CAAGCATGGA ATTTTGTAAA AGAGCATGGG AAATCCAATA AGAAAAGATG GAAAAATGCT CCTCTTGCCG GTTTGAATGC AAATTGGTCT AAGGTTGTAA 3100
TTGATAAAGA TTCCGGAACT GTAAATCATC GAGCATATAC GTTTTGGATG CTCGAACAAG TATTAGAAGC TTTGCACCGA CATGATCTAT ATATAGTAGG 3200
AAGTGAAAAA TATGGGGACC TTCGCGCACA ATTATTACAA GACGAAGAAT GGAAAAGTAT TCGTCCTAGT ATTCTTCGCT CATTAGACTG GTCAATAGAT 3300
TCTTATGAAT CATTGACACC GTTAAAAGAA GAGTTAGACA AAACTTATCA TCAAGTCATT GAGAATTGGG AGAATAATCC TGCGGTGCAA ATAGACACAT 3400
TTGCAGGTAA AGAGAGAATT GTTTTGACAC CTTTAGACAA ACAACCAGAA CCTGAATCAC TACAAAAACT AAAACAACAA ATACATACGA TGTTGCCAAA 3500
TATAGATATT CCTCAATTAT TACTCGAAGT AAATCGTTGG ACGGGATTTA TGGATGGTTT TCGACATATT AGTGAGGCTA AATCTAGAAT TAACGAGTTA 3600
CCTATAAGTA TCTGTGCATT GCTTATATCT CAAGCATGCA ATATTGGGTT AAGACCTTTA GTTCAAGATG GGGTTCCTTC ATTAGAACGT GATCGTCTTA 3700
CATGGATTGA ACAAAATTAT TTTCGTGCAG AAACACTTTC AGAATCAAAC GCGAAACTTG TAGATTTTCA TAGCCAATTA CAGCTGGCTA AAATGTGGGG 3800
TGGTGGAGAA ATTGCTTCAG CTGATGGATT ACGTTTCATC ACACCAGTAA AATCCGTACA CACTGGTCCA AATCCTAAAT ATTTCGGTTC TGGTCGTGGT 3900
GTTACGTATT ACAACTATAC GAGCGATCAA TTTACCGGAC TCCACGGTTT GGTGATTCCA GGCACAATTC GTGATTCATT ATACTTACTT CAATGTGTGT 4000
TAGAACAAAA TACGAACTTA CAGCCAAAAG AAATTATGAC AGATACAGCT GGGTATAGTG ATATTATTTT TGGGCTCTTT GGATTATTAG GATATCAATT 4100
TAGTCCTCGT TTAGCTGATA TCAGTGAATC ACGTCTTTGG CGTTTTGATG CGAACTCAGA TTATAGCATG TTAAATAATT TGTCTAAAAG TCGCATTCGT 4200
GAAGAACTCA TACATCGTCA TTGGGAAGAC ATGCTTCGTG TTGCGGGATC TTTGAAACTA AATAAAATAA ATGCAACACA TCTTATCCAA GCACTTCAGT 4300
ATAATGGGAA ACCAACTATG TTAGGGCGAG CAATTGGAGA ATTGGGGAGA CTCTTTAAAA CACGTTATTT ACTCTTATAT TTACATGATG AAAATTATCG 4400
TCGTAAAATT TTAAATCAAC TCAATAGAGG GGAAGCAAGG CATAGTTTAG CGAGGGCTGT ATTTTACGGC AAACGTGGAG AACTTCATCA ATCCTATCGA 4500
GAAGGACAAG AAGAGCAATT AGGTGCATTA GGTTTAGTAG TAAATGCAAT TATTGTATGG AATACACGAT ATATAGAATC TGCGTTACAA GTACTCCGAA 4600
ATCGCGGTCA TACAATTGAT AATGATGATA TATCTAGACT TTCACCATTA GGCCATAAAC ACATTAACAT AGTAGGTCGG TATTCATTTG TTCTCCCAGA 4700
AGAAGTAAAA GATGGGCAAT TACGTACACT AACATATGAA GAAACAAACA AAAAGGAACC TGATTCTTTA TAAGAATAGG TTCCTAATGT CCGCTAATGC 4800
TTGTTGCGTG ATTTTGTTCC ATTGCTACAC ATACCCC

 Recombination Sites     

Name Coordinates Gene Sequence
res_site_d 40-51 12 ATTAGCGGAC AT
res_site_a 639-650 12 ATGTCCACTA AT
res_site_b 655-666 12 ATTAGTGGAC AT
res_site_c 691-702 12 ATGTCCGCTA AC
res_site_d 726-737 12 ATGTCCGCTA AT
res_site_d 4787-4798 12 ATGTCCGCTA AT

 ORFs     
ORF Summary
Gene Name Associated TE Coordinates Class Sub Class Orientation
parE Tn5401 119-343 Passenger Gene Toxin -
parD-noDBD Tn5401 351-608 Passenger Gene Antitoxin -
tnpI Tn5401 764-1684 Accessory Gene Resolvase +
tnpA Tn5401 1756-4773 Transposase   +

ORF Details
Gene Name Protein Name Associated TE Gene Length Coordinates Strand
parE ParE Tn5401 225 119-343 -
Class:   Passenger Gene
Sub Class:   Toxin
Function:   unknown
Target:   DNA gyrase
Sequence Family:  ParE_toxin (Pfam:PF05016)
Protein Sequence:  
MKFIAKQEKG IQKRIAEGLK GLLKIPPEGD IKSMKGYTEL YRLRIGTFRI LFEINHDEKV IYIQAIGNRG DIYK

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
parD-noDBD ParD-noDBD Tn5401 258 351-608 -
Class:   Passenger Gene
Sub Class:   Antitoxin
Function:   unknown
Sequence Family:  parD (PDB:4Q2U)
Comment:   no PBD
Protein Sequence:  
MAIRKDELYR LIDHLDQQDE KAAFDFLEFL VQRSRRKPKE WEKIDMADPD HEPLSTQELE QLNSEEGYVS GEDAKREFGL QIDLP

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
tnpI TnpI Tn5401 921 764-1684 +
Class:   Accessory Gene
Sub Class:   Resolvase
Function:   cointegrate resolution, transcriptional regulation
Transpoase Chemistry:   Tyrosine
Sequence Family:  Tyrosine Site-Specific Recombinase
Comment:   belongs to the phage integrase family of site-specific recombinases
Protein Sequence:  
MHSTKTISIQ ATSLISDFIS SLSQEGDLHT KTLKEYTSDL KDFVFWFENV WGKHAEDTLF HPIEVTARTI ARYRGHMQVT RLLKPSTINR RINSIKRYFD
WAKQKGLVQT NYSKSIKFVP TEKTSPKRMS DKEEAALMHA VEKYGTLRDR AMIIFMLHTG LRSMEVCDVQ IEDVIMRKRG GYVVVRSGKR NKQREVPLNS
TARCALEEHI RLSEISQSYL FPSSKTGKRL QERAIRHILQ KYIRLAKLEG FSAHDLRHRF GYVMAERTPL HRLAQIMGHD NLNTTMIYVR ATQEDLQGEV
EKIAWN

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
tnpA TnpA Tn5401 3018 1756-4773 +
Class:   Transposase
Function:   cointegrate formation during transposition
Transpoase Chemistry:   DDE
Protein Sequence:  
MPVDFLTPEQ EEKYGCFCDT PTSEQLAKYF WLDDTDKELI WNRRGEHNQL GFAVQLGTVR FLGTFLSDPT NVPQSVITYM ANQLHLDAQS FSRYRNKRSQ
WDQMQEIRSV YGYKNFTDKS THWRFIRWLY ARAWLYNERP SVLFDLATAR CIEQKILLPG VSVLTRLVST VRDRSAENIW KKLSSLPDNV QKKQLENLLQ
IDQKTKKTYL ERLSNPPVPI SVTGIKNTLI RLQELRQLNT ENWDMSRIPS KRLQQFARHT VAVRSQAIAR MPDQRRMAML VAFAKMYTQS AQDDVIDIFD
RYLTDLFAKT YRKEQKERLR TIKDLDKAAR QLREACVILL EHTDPSVHPK TAVFEKISEK DLIQAVQIVD SLTYSPNQTL AYSGLLQHYG IIRKFLPLLM
EEIELQATPA GLPILQAWNF VKEHGKSNKK RWKNAPLAGL NANWSKVVID KDSGTVNHRA YTFWMLEQVL EALHRHDLYI VGSEKYGDLR AQLLQDEEWK
SIRPSILRSL DWSIDSYESL TPLKEELDKT YHQVIENWEN NPAVQIDTFA GKERIVLTPL DKQPEPESLQ KLKQQIHTML PNIDIPQLLL EVNRWTGFMD
GFRHISEAKS RINELPISIC ALLISQACNI GLRPLVQDGV PSLERDRLTW IEQNYFRAET LSESNAKLVD FHSQLQLAKM WGGGEIASAD GLRFITPVKS
VHTGPNPKYF GSGRGVTYYN YTSDQFTGLH GLVIPGTIRD SLYLLQCVLE QNTNLQPKEI MTDTAGYSDI IFGLFGLLGY QFSPRLADIS ESRLWRFDAN
SDYSMLNNLS KSRIREELIH RHWEDMLRVA GSLKLNKINA THLIQALQYN GKPTMLGRAI GELGRLFKTR YLLLYLHDEN YRRKILNQLN RGEARHSLAR
AVFYGKRGEL HQSYREGQEE QLGALGLVVN AIIVWNTRYI ESALQVLRNR GHTIDNDDIS RLSPLGHKHI NIVGRYSFVL PEEVKDGQLR TLTYEETNKK
EPDSL

 References     

Baum JA. Tn5401, a new class II transposable element from Bacillus thuringiensis. J Bacteriol. 1994 May;176(10):2835-45. doi: 10.1128/jb.176.10.2835-2845.1994. PubMed ID: 7514590