Transposon
Name: Tn5406
Family: Tn554
Evidence of Transposition: yes
 Host     

Host Organism:Staphylococcus aureus MRSA Molecular Source:chromosome
Place of Origin:Spain Date of Isolation:January 2011
Other Geographic Information:human skin lesion

 Map     



 Sequence     
DNA SequenceLength  5473 
--------10 --------20 --------30 --------40 --------50 --------60 --------70 --------80 --------90 -------100
GATGTATTAA ACGTAGTATA CTAATCTATA GTACTTAAAG TATTTAAAGA AAGTATAATG GATGATATAC TACTTTGGGT ACATTATATC AATAGGAGAA 100
ATATAAAGTA TATAAAGTAT TCAAAGTGGG GGAGGAAAAA TGAAAGTGCA AAAAATAGTA GTGGATAATA AAGCTTATCC ACTATTTATA TTGCTTGATG 200
AACAATTTGA AGTAGTTGAA CCGGTTATGA GCTTCATTAA ATATCTAGAT AATACTAATA AGTCACCCAA CACTATAAAA ACATATTGTT ACCACCTAAA 300
GTTATTTTAT GTGTTTATGC AGCAAAGAAA AATCTCGTTA GACGAAATTC AGTTTGACGA GTTGGCGAAT TTTGTAGGAT GGTTACGTAA CCCCACAGAA 400
AACGCGAATG TTATTGACAT TCACCCAAAA GAAGCTAAAA GAGAGGAATC TACTGTTAAT GCTATTCTTA ATGCCGTGAT TAGTTATCTA GAATATTTGA 500
GTCGTTCTGG TGGCTTTAAA ATGCTTGATT TGTTCAATGA AACACGAGGC AGAAACTACA AAGGATTTCT CCATCATGTG AGTAAAGGAA AGCCATATAA 600
AAGAAACGTA TTGAAGTTAA GGGAAAAAAA GAAAATGATT AGGACACTAA ATCATTCAGA GGTAAAAGAA ATCGTAGAAG CCTGTCACAC CCTCAGAGAT 700
AAATTAATCA TAATGCTTAT GTATGAAGGT GGGATGCGAA TAGGAGAGGT TTTGTCTCTA AGACTGGCAG ACATAGTGAC TTGGGATAAT CAGGTTCACA 800
TAACACCTAG AGAAGAAAGT CTGAATGGAG CTTACATAAA GCTTAGAAAA GAAAGAGTAA TCCATGTTAG CAAAGAGTTA ATGGCTCTCT ATACAGACTA 900
TCTTGTGCAT GAATACTACG ATGAATTAGA GCATGATTAT GTATTTATAG CATTAAAAGA ATCGCATTTT GGGCAGCCTT TAAAATATCA AAGTGTACTC 1000
GATCTCGTTC GGCGGTTGAA TAAAAGAACA GGTATTGTGT TTACACCTCA TACGTTACGC CATACCCATG CGACAGAACT GATTAGAAAT GGTTGGGATG 1100
CTGCTTACGT CCAAAAAAGA TTAGGACACG CACAGGTTCA GACCACTTTA AACACATACG TCCACCTCTC TAACCAAGAT ATGAAAGAAG AATTTAAAAA 1200
GTATCTTGAA GGGAGAGATA AATGACGATG AATACCAAAA GAAAAATTAT AAGCTCTGTA GCAATTGGTA AAAAAATAGC AGAAATGAAC AGCAAATTAG 1300
AAGGATATTG GGCTGATGAT AGATGGGATA TCAGAAAGTG CCCACTACCT TCAGCAATCG AACTTTCTAA AAGCCCATCT TTAAGAAACC GATGGGTAAA 1400
TTTTGACCGA GTTGAAAATT TGTGGTTAAG AACCGAATTG AAATTCTTTT TCTATTACCA CATGACCAAT GAGGTTTGGA ATGCTAAAAC CGTGTGGATT 1500
AGAAAAGGAA CTGTAATTAA TAAAATGTTG GGTTTCTTAG ATATGAAATA TCCTCACATA GAGTCAATCA CAGAAGTACC AATTGAAAAA GCTATGACTG 1600
AATACAGGAC TTACTTAGTA GAGCAAGGAG TCAGAATAAC AACTACCAAT CACAAGCTAA ATGCCAAACA AGAAAGAATC ACAGTAAAGG CAAATTCATA 1700
CTATGTGACA AATCTTAAGC AGTTTATGGA GTTTTATGAA GATTATTATT TTGACGGAGA AGAATGGGAA AAGGATGTTT GGGATAGAAG AAAAATGAAT 1800
CTCCCTTCTG ATAAAGTCAA TCCCACTCAA TATGAGTATC TCGTATCTTT CAAAGAGATT CCTAGTATTT ATTACAGAGA GCTGACAAAA CGATATTGCA 1900
AGCTCAAATT AAACACCGTG AGCTTTTCTC ATGTAAGCGA TATCGCAGGC AGGTTGAAAG AGTTTTTTGT ATTTCTTAAT AAAAATTATA AACATTTAAC 2000
AAGACTTCAT CAGCTTACCC GAGAGCAAAT TGAACACTAC TTGGCAGAAC TGAATAAATC AGGAATTAAA CCGAGCACTT TAATGGGGAA AATATCGGTT 2100
TTGGACGGTT TCTTTACTAC AATTCAGAAG TTTGATTGGA ATGACGTTCC TTCAAAGATA CTAGTTTTCC AAGAAGATTA TCCTAAGGTA CCGAAAGCAA 2200
CACCGAGATA TATTGATGAA TACGTTTTGG AGCAATTAAA CAGTCATTTA GATGATTTAC CTGCTTATAT AGCAACTATG GTAATGATCA TTCAAGAAGG 2300
TGGTATGAGA ATCAGTGAGT TGTGTACTTT GAAAAGAGAT TGCCTTCTCG AAGATAAGGA AGGTGATTAC TTTTTAAAAT ATTACCAATG GAAAATGAAA 2400
AAAGAACATA CTATTCCGAT ATCGAGAGAG GTAGCTGGTC TTATTAAGGC ACATGAAAAG CATGTGTCAG AGGAGTTTGG TGGATGTGAA TACCTCTTTC 2500
CTCGTAAAGA TGGCTCTCCA TTGAAACAGG ATACTTTTAG ACGGGAACTA AACGAGGTGG CACATAAGAA AAATATCGTG GATCGAGCAG GAAGCGTTTT 2600
TAGATTCCAC GCACACGCAT TTCGGCATAC CGTTGGTACA AGAATGATTA ATAATGGCAT TCCTCAACAT ATTGTCCAGA AATTTTTAGG ACATGAAAGC 2700
CCGGAAATGA CGAGCAGATA TGCCCACATT TTCGATGAAA CATTAAAGGA AGAGTTCTCT AAATTCAAAG AGACGCTTGT GACAAATCAG GGCAGCATTA 2800
TTGACATAGA AGAATCCGAA GAAGCCAATA AAACTGATCT TCAATGGTTC AAGAAGAACA TTAACGCTCA GGTATTGCCC AATGGCTATT GTCGACTCCC 2900
GATAATCGCT GGTCCTTGTC CTCACGCCAA TGCTTGTTTA GACTGCACAC ACTTCTGTAC AAGCAAAAAG TTCTTATCGC AACATAAAGA TCACTTAGCT 3000
CATACTAAGG AATTATTAGC TATCGCAAAA GAGAAACAAT GGCAACGACA GATTGAAACC AATTCTCGTG TACAAGAGCG ACTAGAGCAG ATAATAGGCA 3100
GCTTAAAGGA GACGGAGTAA ATGGGGAAAC AATCAAGGAA TACTGATAAG ATTATTCAAC TGGCAAAAGA AAAAAGTCAC AATACTAGAC TAAATGTAGA 3200
AAAGATAATT TCAAAAATGT CATTAGAAGG CAAAACTATA AATTTTAATA CAGTAGCTGC AGAAGCAAAA GTCTCGAAAT CTTGGTTGTA TAAAGAAAGT 3300
GATATAAGAA AACAAATTGA AAATATCCGA CATCGCCAAC TCAATGGAAA AAGATTGAAC TTTACGCCTA TAAAGAAAAA TAAAAAATCA GAAGAAATAC 3400
TTATCGAAAC GCTAAAAGCG AGGATAAAAG AATTAGAGGA AGAAAATGGT CAATTGAAAA ATCAAGTTCA GAAATTATAT GGTGAGCTTT ATTTTAAAGA 3500
CTAGAAAGAA TACTCTGACT TAAACATTTG ACATTTCCCC GTCATTTGTT TAAGGTAAAT TTAATTAGAC GAAGGAAAGG GTGAACCAAC TACATGATTA 3600
ACTAATCCTA TTTTTGAAAG TAAACAATCG AAGGTGTTTG ATTTACAAAT GATGTTTTAT TTGTGCTGCC TTCAATTGTG ATCTTCAGGA TAGGATTAAA 3700
TTTCTGTAGT TGGCTCTAAA AGAGTCTTTT TTAGAGTACA TCTATATTGA TTTATGCCTC CTATTCTGAA TGAATTAGGA GGCATTTATT GTCTCCGATT 3800
ATTTTTAAGG GGATGATAAT ATGAAAATAT TGTTAGAGGC TCTTCGTATA AAACCCTATG TTCAAGATCG TTTACTGTTG AACATAGATC AATTACAGAT 3900
TTATCAGAAT GACCGAATTG GGTTAGTTGG TGGAAATGGC AGTGGAAAAA CAACGTTACT TCACATATTG GATGAAAAGC TTTTTCCTGA AGAAGGTACT 4000
GTAACTCAGT ATTCACGGTG CGAACTCATT CCACAATTGA AACATATGGA AACAACAAAA AGTGGTGGTG AAGTAACACG AAAATATATT CAGCAAGCAC 4100
TTGATAAAAA CCCAGAACTG TTACTAGCAG ATGAACCGAC AACTAACCTT GATACAAATT ATATAGAAAA CTTAGAGCGA AAATTAAAGG ACTGGCATGG 4200
AGCATTTATC ATCGTTTCAC ATGATCGTGC TTTCTTAGAT ACTCTTTGTA CGAGTATATG GGAAATCAAA GACGGGGGTA TAACCGAATA CAAAGGGAAC 4300
TATAGTGACT ATATTGAGCA GAAAGAATTA GAAAATCGCC AAGAGCAATT AGCACATGAA AAATATGAAA AAGAAAAGAA ACAGTTAGAA GAGGCCATAA 4400
AGTTAAAAGA AGAGAAAGCT CAACGAGCTA CTAAGAAACC GAAAAATATA AGTTCATCGG AAGCAAGGCT AAAAGGAGCG AAGCCATACT TCGCAAATAA 4500
ACAGAAGAAG TTACGGAAAA CGGCAAAAGC TCTAGAAACT AGACTGGATA AGCTTGAAAA GGTAGAAAAA ACAAAAGAAC TACCCCCACT TAAAATGGAT 4600
TTATTGAATT CAGAGACTTT TAAAAATCGG ATTATACTCC GTGTTGAAGA TGTTTCGGGT GTAATTGAGG AACGAGTATT GTGGAAAGCA GCTAGTTTTT 4700
ACGTTCGAGG AGGAGATAAG CTGGCAATTA TCGGCTCTAA CGGTACGGGC AAGACCACCT TTATTAAAAA AATTGTTCAG GATAAGCCAG GTATTTCATT 4800
TTCACCATCT GTTAAAATTG GTTACTTTAG CCAGAATCTA GACATATTAG AGCTCGACAA GACTATTTTA GAAAACGTCC AATCTTCTTC ACGGCAAAAT 4900
GAAACTCTTA TTCGAACCAT TCTAGCGAGA ATGCATTTTT TCAGAGATGA TGTTCATAAA CCAGTAAATG TCTTAAGTGG GGGAGAGCGA GTTAAGGTAG 5000
CACTAACTAA AGTGTTCTTA AGTGATGTTA ATACGTTAGT ATTAGATGAA CCAACAAACT TTCTTGATAT GGAGGCTATA GAGGCGTTTG AATCCTTATT 5100
AGAGGAGTAT GAAGGAAGCG TAATTTTTGT CTCCCATGAT CGTAGGTTTA TCGAAAAAAT AGCTACCCGA ATCATGATGA TTGATAATAA AGAAATTAAA 5200
ATATTTGAAG GAACATATGA CCAATTTAAA GCTAAACAAG CTAGGGAGGA AACACGGGAT ATAAAAGAGG ATAAAAAACT TTTACTTGAA ACAAGGATTA 5300
CTGAGATACT CAGTCGATTG AGTATTGAAC CTTCGGAGGA ATTAGAAAAA GAGTTCCAAA ACCTAATTAA CGAGAAAAGA AATTTAGATA ATTGAATCAC 5400
TTTAAGGACA TGTCTTTAAA GTGTAAAGGT TATTACAATC GGCTTTTTTA TGGATTACTC TTGATATGAT GTA

 Recombination Sites     

Name Coordinates Gene Sequence
att 1-6 6 GATGTA

 ORFs     
ORF Summary
Gene Name Associated TE Coordinates Class Sub Class Orientation
tnpA Tn5406 140-1225 Transposase   +
tnpB Tn5406 1222-3120 Transposase   +
tnpC Tn5406 3121-3504 Accessory Gene Helper +
vgaALC (ARO:3002830) Tn5406 3821-5395 Passenger Gene Antibiotic Resistance +

ORF Details
Gene Name Protein Name Associated TE Gene Length Coordinates Strand
tnpA TnpA Tn5406 1086 140-1225 +
Class:   Transposase
Comment:   tyrosine recombinase XerD?||TIGR02225||phage integrase, N-terminal SAM-like domain||DNA breaking-rejoining enzyme C-terminal catalytic domain
Protein Sequence:  
MKVQKIVVDN KAYPLFILLD EQFEVVEPVM SFIKYLDNTN KSPNTIKTYC YHLKLFYVFM QQRKISLDEI QFDELANFVG WLRNPTENAN VIDIHPKEAK
REESTVNAIL NAVISYLEYL SRSGGFKMLD LFNETRGRNY KGFLHHVSKG KPYKRNVLKL REKKKMIRTL NHSEVKEIVE ACHTLRDKLI IMLMYEGGMR
IGEVLSLRLA DIVTWDNQVH ITPREESLNG AYIKLRKERV IHVSKELMAL YTDYLVHEYY DELEHDYVFI ALKESHFGQP LKYQSVLDLV RRLNKRTGIV
FTPHTLRHTH ATELIRNGWD AAYVQKRLGH AQVQTTLNTY VHLSNQDMKE EFKKYLEGRD K

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
tnpB TnpB Tn5406 1899 1222-3120 +
Class:   Transposase
Comment:   C-terminal catalytic domain cd01187
Protein Sequence:  
MTMNTKRKII SSVAIGKKIA EMNSKLEGYW ADDRWDIRKC PLPSAIELSK SPSLRNRWVN FDRVENLWLR TELKFFFYYH MTNEVWNAKT VWIRKGTVIN
KMLGFLDMKY PHIESITEVP IEKAMTEYRT YLVEQGVRIT TTNHKLNAKQ ERITVKANSY YVTNLKQFME FYEDYYFDGE EWEKDVWDRR KMNLPSDKVN
PTQYEYLVSF KEIPSIYYRE LTKRYCKLKL NTVSFSHVSD IAGRLKEFFV FLNKNYKHLT RLHQLTREQI EHYLAELNKS GIKPSTLMGK ISVLDGFFTT
IQKFDWNDVP SKILVFQEDY PKVPKATPRY IDEYVLEQLN SHLDDLPAYI ATMVMIIQEG GMRISELCTL KRDCLLEDKE GDYFLKYYQW KMKKEHTIPI
SREVAGLIKA HEKHVSEEFG GCEYLFPRKD GSPLKQDTFR RELNEVAHKK NIVDRAGSVF RFHAHAFRHT VGTRMINNGI PQHIVQKFLG HESPEMTSRY
AHIFDETLKE EFSKFKETLV TNQGSIIDIE ESEEANKTDL QWFKKNINAQ VLPNGYCRLP IIAGPCPHAN ACLDCTHFCT SKKFLSQHKD HLAHTKELLA
IAKEKQWQRQ IETNSRVQER LEQIIGSLKE TE

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
tnpC TnpC Tn5406 384 3121-3504 +
Class:   Accessory Gene
Sub Class:   Helper
Sequence Family:  Tn554_family
Protein Sequence:  
MGKQSRNTDK IIQLAKEKSH NTRLNVEKII SKMSLEGKTI NFNTVAAEAK VSKSWLYKES DIRKQIENIR HRQLNGKRLN FTPIKKNKKS EEILIETLKA
RIKELEEENG QLKNQVQKLY GELYFKD

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
vgaALC (ARO:3002830) VgaALC Tn5406 1575 3821-5395 +
Class:   Passenger Gene
Sub Class:   Antibiotic Resistance
Function:   antibiotic target protection (ARO:0001003)
Target:   streptogramin antibiotic (ARO:0000026)||pleuromutilin antibiotic (ARO:3000670)||lincosamide antibiotic (ARO:0000017)||oxazolidinone antibiotic (ARO:3000079)||tetracycline antibiotic (ARO:3000050)||phenicol antibiotic (ARO:3000387)||macrolide antibiotic (ARO:0000000)
Sequence Family:  ABC-F ATP-binding cassette ribosomal protection protein (ARO:3004469)
Comment:   loose match to reference sequence for ARO:3002830 (bitscore: 833)
Protein Sequence:  
MKILLEALRI KPYVQDRLLL NIDQLQIYQN DRIGLVGGNG SGKTTLLHIL DEKLFPEEGT VTQYSRCELI PQLKHMETTK SGGEVTRKYI QQALDKNPEL
LLADEPTTNL DTNYIENLER KLKDWHGAFI IVSHDRAFLD TLCTSIWEIK DGGITEYKGN YSDYIEQKEL ENRQEQLAHE KYEKEKKQLE EAIKLKEEKA
QRATKKPKNI SSSEARLKGA KPYFANKQKK LRKTAKALET RLDKLEKVEK TKELPPLKMD LLNSETFKNR IILRVEDVSG VIEERVLWKA ASFYVRGGDK
LAIIGSNGTG KTTFIKKIVQ DKPGISFSPS VKIGYFSQNL DILELDKTIL ENVQSSSRQN ETLIRTILAR MHFFRDDVHK PVNVLSGGER VKVALTKVFL
SDVNTLVLDE PTNFLDMEAI EAFESLLEEY EGSVIFVSHD RRFIEKIATR IMMIDNKEIK IFEGTYDQFK AKQAREETRD IKEDKKLLLE TRITEILSRL
SIEPSEELEK EFQNLINEKR NLDN

 References     

Haroche J, Allignet J, Buchrieser C, El Solh N. Characterization of a variant of vga(A) conferring resistance to streptogramin A and related compounds. Antimicrob Agents Chemother. 2000 Sep;44(9):2271-5. doi: 10.1128/AAC.44.9.2271-2275.2000. PubMed ID: 10952567