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Terminal Inverted Repeats | |
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Internal Transposable Elements | |
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Internal Repeats | |
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| Name: Tn558 |
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| Family: Tn554 |
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| Evidence of Transposition: yes |
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| Host |
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| Host Organism: | Staphylococcus lentus | Molecular Source: | pSCFS2 |
| Place of Origin: | USA | Date of Isolation: | 2004 |
| | Other Geographic Information: | nasal swab of a calf suffering from a respiratory tract infection |
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| Map |
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| Sequence |
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--------10 --------20 --------30 --------40 --------50 --------60 --------70 --------80 --------90 -------100
GATGTATTAA ACATAGTATC CTAAACTAGA GTACTCTAAG TACTCGAAGT TTAGGATTTT TTAATTACAG TGCTTTAACT ATTAAATATA TAAGGGTATT 100
ATTAATAGTA GTTAAAGTAT TTAAAGGTGG TGGAAAGATG AAGGTTCAGA AAGTAATTGT GGAGGAAAAA TCATATCCGT TATACATACT GCTAGATAAA 200
GAATTTGAAG TGATAGAACC GGTTAAGCGA TTTATAAAGT ACTTGGATAA TACGGGCAAA GCTCCAAATA CCATTAAAAC ATATTGTTAT CATCTCAAGC 300
TGTTTTATGA ATTTATGAGC CAAAGTAGAA TCGAATTAGG AGATTTACAA TTTGAGGATT TAGCAAACTT TGTAGGATGG TTAAGAAATC CAGCAGGGCA 400
TTTAAAGGTA ATAGATATAC AACCAAAGAA GGCTAAAAGA GAGGAAACAT CAGTTAATTC CATACTTAAC GCTGTAACTA GTTTCTTAGA GTATTTAAAT 500
CGCACAGAAA ATTTTAAAGC TATAGATATG TCTAAAGAAG CAAGAGGAAG AAACTTTAAG GGGTTTCTTC ACCATATTTC TAAAGGTAGA TCCTATAAAA 600
AAAATATTTT AAAGCTTAGG GTCAAAAAGA AACTTGTACA AGTATTAGAA CATGGACAAG TCAAAGCAAT AATTGAGGCA TGTCATACCA AAAGAGATAA 700
GTTACTTATT ATGCTTATGT ATGAAGGGGG ACTTCGGATA GGAGAAGCAT TATCCCTTCG TATTGAAGAT ATTTCAACAT GGGATAACCA GATTAACATC 800
AGGCCAAGAG ATCATAATGA AAATGGAGCT TATATTAAAC TTAAAAAAGA AAGAACTATT GATGTAAGTA AGGAATTAAT GGCATTATAT ACCGATTACT 900
TAGTACATGA ATATGGGGAA GATTTAGATC ATGATTATAT ATTTATTAAT CTTAAAGATT CTTATTTTGG CCACCCTCTA AAATATCAAA GTGTATTAGA 1000
CTTAATAAGA AGACTAGGAA AACGGACAGG GATTACTTTC ACTGCCCATA TATTACGTCA TACGCATGCC ACAGAGCTTA TTAGAAGTGG ATGGGATGGT 1100
GCATATGTAC AAAAAAGATT AGGGCATGCC CATGTACAAA CAACACTTGA TACGTATGTT CATCTTTCTG ATCAAGATAT GAAGAATGAA TATAAAAAGT 1200
ATCTTCAAGG GAGAGAAACA TGACAATGAA ATTTCCAAGT GTAGCAACTA ATCGAAAGCT TATCGCTAGT ACAGAGATTA ATAAAAAAAT AGCTAATATG 1300
ACAAGTGTTT TAAAAGGTTA TTGGGCAGCA GATAGATGGG ATATAAGAAT TTGTCCGCAT CCTAGTGCAA TTGAGTTAAG TAAGAATCCG TCACTAAGAA 1400
ATCGTTGGGT AAATTTCGAT AAGGTGGAAA ATGTCTGGTT GAAAACAGAA TTAAAATATT TTTATTACCT TCACTTGAAT AATGGAGCTT GGAATGCAAA 1500
ATCCGTTTGG ATTAGAAAGG GAACAGTGAT AAGCCGGATG ATGGGATTTT TAAATTTAAA ATATCCTAAT ATTACATCGA TAACCGAAGT GCCTATAAAA 1600
AAAGCTTTGA CAGAATACCG GACCTACTTA ACAGAACAAA AAGTAAAAAC TACGACTACC AATTACAAAC TTGATGTAAA TCAGCAGAAA GTTACTGTAC 1700
ATGCGAATTC CTATTACGTT ACTCATCTTA AGCAGTTTAT GGAATTCTAT GAGGACTTCT ATTTTGATGG GGAAGAATGG GAAAAAGATG TTTGGAATCG 1800
AAGAAAATTA TCATTACCGG AAGATAAGGT AAACCCAACA TCCTACGAAT ATACGATCAA CTTTAAGGGT TTTAAGAATA ATTATTTTAA AGAAATAGTT 1900
AAGCGATATT GTAAACTAAT GTTAAACACA GCTAGCTTTT CTCACGTAGT AGATATAGCT TCAAAATTAA AAGAATTTTT TAATTTCATG AACAAAAATT 2000
GTGAAGGTAT ACAAAGGATT CATCAATTAA CTAGAAATGA AATTGAGCAA TATTTTAATT ATATTAATTT AAAAGGTTTA AAACCCAGTA CTGTAACTGG 2100
ACGAATATCT ACTTTAGACG TTTTTTTTAC TACAATTCAA AGATATGACT GGAAGGATAC ACCTTCTAAG ATCCTTATCT TTCAAGAAGA TTACCCTAAA 2200
GTGCCGAAGG CACTACCACG TTATATTGAT GAACATATAC TTGAACAATT AAATGGGAAA TTAGATAAAT TGGAACCTTA TATTGCTACA ATGGTTATGG 2300
TACTTCAAGA ATGCGGGATG CGTATCAGTG AACTTTGTAC ATTGAAAAAA GGGAGCGTCA TAACCGATAA AGAAGGGGAT TGCTTTTTAA AGTATTATCA 2400
GTGGAAAATG AAGAAAGAGC ATATCATTCC TATTTCTAAA GAAATTGCTG CATTGATATT AGTTCAAGAG CAAAGGGTGG CTGATGAACT CGATGATGGA 2500
TGTGTATATG TGTTTCCCCG AAAAGATTGC TCACCATTGA AACAAGATAC CTTTAGGGTT AAATTAAATG AACTAGCTTA TGAAGAAAAG ATAACGGACA 2600
GCAACGGAGA AATTTTTCGT TTTCATGCTC ATGCCTTTCG GCATACAGTT GGCACTAGAA TGATAAATAA CGGAGTGCCA CAACATATTG TCCAGAAGTT 2700
CTTGGGTCAC GAATCACCGG AAATGACGGC AAGATATGCA CATATTTTTG ATGAAACCCT AAAGAAGGAA TTTACGAAAT TTAAGGAAAC CTTAGTAACG 2800
AATAACGGTA GCATTCTGGA TTTAAGTGAG GAAAATACTG AAGCTGACAA TACAGATCTT CAATGGTTTA AAAAGAATAT CAATGCACAG GCACTTCCTA 2900
ATGGCTATTG TCGGTTACCA GTAATTGCAG GACCATGTCC TCACGCAAAT GCATGTTTAG ATTGTACGAA TTTCTGTACA AGTAAACAAT TTCTTACTGA 3000
ACATGAAGAG CACTTAGAGC GAACTAAAGA AATACTAAAT AGGGCTAAAC AAAACCAATG GCAGCGTCAG GTTGAAACCA ATGAACGTGT TAAAAATAGA 3100
TTAGAACAGA TTATTCATTC GTTAAAGGAG ACGAATTAAA ATGATTAGAA AAGGTAACAC AACTGCCATA GTTCAGCTAG CTAAAGACAA GTCGGAGAAA 3200
ACAAGAATTA GGGTTGAAAA GACAATTTCA GAGATGGCAT TGAAAGAAGA GAAGATTAAT TTTAATTCCG TTGCACAAAA AGCAAATGTT TCAAAGTCAT 3300
GGCTTTACAA ACAAAAAGAT ATTAGAACTA GAGTGGAGAC ATTAAGAGGG ATGCAGATAA GTGAGTTAAC CCCCCGTAAA CCTAGTAAAA GCCCTCGTTC 3400
AGAGGACGTA TTAATAAAAA CCTTAAAAAG CCGTATAAAG GCGTTAGAAG AAGAGAATGA ACGGTTAAAG GATCAAGTTC AAAAATTACA TGGCAAGCTG 3500
TTTTAGCAGA TTTGTGTTTC TTGGAATTTA TTGGGCACTT TGAATTGGCT ACCTAAAATG AAATCGCTAA AACCTTCAAT AACTTCAATA GCCCATTTCC 3600
CTAAATGTGT TAAGGGGAAA TGGGCTTTCT TCTAGTATTG TTGGCATGAT CGCAGAAGTG TTTTATGCTC TTAAATAATA CTTTTTAATA TATTGCAAAT 3700
ACTCATTAGC ACTTTTCTGT ATCTCTTCGC CCTTCATATC CGAATTAGCA CCGTAAAGTA CAAACTCTGG TACATATTCA GCATGAATCT ATGCACATAA 3800
AGATTTGAAT GGTGTTAACA TCTGGGTTAA TGTATGCTTG TTTTTACCCA TACTTGTAAA TTCACCTTTT TTTACGCCAG CTGATATAGC TAATCCTAAT 3900
TTTCGATTAT AAAATATTCT TTTACCCTTT GATCCGTAAG CCCATCCATA TATAATCACT TCATCGATCC ATTTTTTTAA TAATGAAGGA GAACTATACC 4000
AATATAATGG AAATTGAAAA ATAATATTAT CATGATTTTC AACTAATTCC TGCTCTCTTT TTACATTTAT AATAAAATCA GGATACTCTC TATAAAGATC 4100
ATGAATGGTA ATTTCGTTTG AATAAGACGC TGCTTTTTCT ACCCAAACTT TATTGATTCG AGAATTTGGC ATATCTGGGT GAGAAACGAT CACCAATGTT 4200
TTCATTGTTT CATCCTTAAC ATACTCAACT TTCGCACCAA TAAAACAGTG TACGAAAGTT GAGTTACTTA AAAGTATTCT ATTCTAAGAA ATTCAAATTT 4300
GCGTGATTCC TAAGCTATTT ATTTACAGCT TAAACTATAG AAGATGAACT AAACAATAAC TAATCTTTAC ATAACTAAGT TATTACCCAC GCTTTTTTAA 4400
ACCTAATCCA GCTATTAAGG CAATGAGTAT TGCCCCTGTA GCTGCAAGGA ACGCATCTGA GTAGGACATA GCGTCCAATA TATATAATGG ATTTATCGGC 4500
TCAGTAGCAT CACGTCGAGC GGATAATAAT GCTCCAATCA TACCTGCTCC AGTTCCTGCT CCAAGGTACA AAGCACCTTG GAAAATCCCC ATTCCGACAC 4600
CAACCTTGTC TGCATCGAGT GCACTTACTG CGGCGTTATT TGCGGGAGAA TTCGTGAATG CAAAAGCAAT CCCTACTCCG AGGACCCCCA CGGAAACTAA 4700
CAGAGGTGAA GCACCAGATG CATAGGTGGA CAAGAATAAG GTAGACAGCC CCATCAGAGT CATCCCAGTA ATTATCAGAC GTTTATCCCC AAATCGATCA 4800
GAAAGACGGC CAACGAAGGG AGATAAGATT GCAACAGCCA CACCACCTGG CAACAATATC ATTCCAGCCT GTCCAGAAGA GAGTCCATTC ACCTCAACGA 4900
CTAGTAATGG GACGAACACA AGAACAGCGA AATAAGCAAA CATCGAAAAA AATGCAATTA TGACCGTATT GACATAATCC TTGTTATTGA ACAGGACAGG 5000
TGGTACAAAT GGATTTTCTG CGGTAACAAT TCTCCAAATA AATCCCACCA AAGCTACAAC AGAACCAATT AGGCTAGTTA ACGATGAGAA CGAAGAAAAA 5100
CCAGAAGTTT CTCCTTGAGT GATGCCAAAA AGGAGTAATC CTACTGTGAG GCCGAGGAAT AAACCACCAA TGAAATCAAA GTTCTTATTG CTTCCTACGG 5200
ATTCTGCCGG TTTAATTGTC GGTAACGCGT AGTAGGCACC AATAACAATC ATAATGGCTA ACAAAAATGT GAACCAAAAC AAGGCATTCC ACCCTAAATA 5300
TTGACCAACT ACTCCACCAA ATATTGGACC AGCAGCAGTT CCAACACCAA TACTTCCTGC GATAATTCCC AAAGCTCCCC CACGTTTTCC TTGTGGGAAA 5400
ACCTTCGAAA TTGCAATGAT TGATAGAACT GGAATTGCGG ACATCCCAGC ACCCTGAACC ATTCTTCCCA AAACCAACAA TGGGAGGTTC GGGGCAATTG 5500
CACATAAAAG ACTACCACTT GCCAGAATCA TAATGGCAAA GATATATAGC TTTCGTAACT CAAAAAAGTC TGAGATTCGA CCATAAATCG GAACTCCAAT 5600
CGCAAGAACA AGTGCAATAC CACTAACTAT CCAACTCACT TGAGATTTCG AAGCTTCTAA ATCTTTGCTT ATTAGTGGAA GTACGGGATT GACTAAATCA 5700
GCCGTAATTG CACCTACAAG TACAGATAGG GAGAGTACCA TCATTAAAAG CCTAGTAGAA CCCCTTTTTT CAGATTGAAT CATTTCTTTA GATTTACTAT 5800
CCTTTTTCAT TTTATTTCCT CCTAAAATAT ATTGTGATTT TAGGAGGCTA AATCCACTGC TTTCACCATA AACCTCACCT CATATCTATT TATATTGTAA 5900
AACCAAATCA ACGAACTCAC CATATTTCTA CAGCATGATT AAAGATTCGG TTCTCCAAAC TAACTGAACT GATCAAACAA AAAAAAGGCA CCAGTTTAAC 6000
AACCGGTGCC TAATCATTCG TATGCATTTT TACAAATGCA ATAGATTCAT AAATTTTTGC CCATTATATA AAAGGAGGCA AAAAGTTTTC CGGTAGTGTT 6100
TCCATTTTTT GTTTTTGTGA AAAAGGACAT ACTGATCCCG TTGTACCTAA ATCCCCTGAA ACTTTTACAT GCTTTCTAAA CTCGACATTA ATGAAATCAA 6200
TTCCCATTAC TTTTTGCCTC CTTTCTCATA TTGTGATAAT AACACAATAA TAATTGATGA AAAAGAAATA ATCAACCCTA CTTTTTTGAA AACCAATTTA 6300
AAGCTTTACT ACTTTTACTT ACATAATAAA GGCAGGTGCA GTATAAACTT TTTTAATATG TCTTCTTAAA CGAGCAGGTA GCGTCAGTTA AAGTAGATAA 6400
TTTAAGATCG AAATCATATT ATAGATATTC CGAAATTGGG CGTGATTGTT GCAGGTCAAA AGCTTAATTC CTCGATAAAA TAAAAAGGAA TTAGTTTTTT 6500
TATTTGTGGT ACATTCTTCT GACCGTAATC AATTGTCATC TAATAATTAC ATTGTATTTT TTCATTTGAT TTAACACGTT AAATATATGT TCTTAAAGTA 6600
AAAACATTGA TGTTAATGGA TTTTTAGTAA TTTACTCTTG ATAAGATCCA ACGCCATCAG TAAACGATAT TATGGTTGGT AAGAGATTAA AGCTTATAGG 6700
GGAATTGCTA AGTATTGATG TA
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| Recombination Sites |
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| Name |
Coordinates |
Gene |
Sequence |
| att |
1-6 |
6 |
GATGTA |
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| ORFs |
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| Gene Name |
Associated TE |
Coordinates |
Class |
Sub Class |
Orientation |
| tnpA |
Tn558 |
138-1223 |
Transposase |
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+ |
| tnpB |
Tn558 |
1220-3139 |
Transposase |
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+ |
| tnpC |
Tn558 |
3141-3506 |
Accessory Gene |
Helper |
+ |
| fla |
Tn558 |
3789-4205 |
Passenger Gene |
Other |
- |
| fexA (ARO:3002704) |
Tn558 |
4383-5810 |
Passenger Gene |
Antibiotic Resistance |
- |
| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| tnpA |
TnpA |
Tn558 |
1086 |
138-1223 |
+ |
| Class: | Transposase |
| Comment: | tyrosine recombinase XerD||TIGR02225||phage integrase, N-terminal SAM-like domain||DNA breaking-rejoining enzymes C-terminal catalytic domain |
Protein Sequence:
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MKVQKVIVEE KSYPLYILLD KEFEVIEPVK RFIKYLDNTG KAPNTIKTYC YHLKLFYEFM SQSRIELGDL QFEDLANFVG WLRNPAGHLK VIDIQPKKAK
REETSVNSIL NAVTSFLEYL NRTENFKAID MSKEARGRNF KGFLHHISKG RSYKKNILKL RVKKKLVQVL EHGQVKAIIE ACHTKRDKLL IMLMYEGGLR
IGEALSLRIE DISTWDNQIN IRPRDHNENG AYIKLKKERT IDVSKELMAL YTDYLVHEYG EDLDHDYIFI NLKDSYFGHP LKYQSVLDLI RRLGKRTGIT
FTAHILRHTH ATELIRSGWD GAYVQKRLGH AHVQTTLDTY VHLSDQDMKN EYKKYLQGRE T
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| tnpB |
TnpB |
Tn558 |
1920 |
1220-3139 |
+ |
| Class: | Transposase |
| Comment: | Phage integrase N-terminal SAM-like domain||Region: Phage_int_SAM_1||cl12235||Phage integrase family||pfam00589 |
Protein Sequence:
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MTMKFPSVAT NRKLIASTEI NKKIANMTSV LKGYWAADRW DIRICPHPSA IELSKNPSLR NRWVNFDKVE NVWLKTELKY FYYLHLNNGA WNAKSVWIRK
GTVISRMMGF LNLKYPNITS ITEVPIKKAL TEYRTYLTEQ KVKTTTTNYK LDVNQQKVTV HANSYYVTHL KQFMEFYEDF YFDGEEWEKD VWNRRKLSLP
EDKVNPTSYE YTINFKGFKN NYFKEIVKRY CKLMLNTASF SHVVDIASKL KEFFNFMNKN CEGIQRIHQL TRNEIEQYFN YINLKGLKPS TVTGRISTLD
VFFTTIQRYD WKDTPSKILI FQEDYPKVPK ALPRYIDEHI LEQLNGKLDK LEPYIATMVM VLQECGMRIS ELCTLKKGSV ITDKEGDCFL KYYQWKMKKE
HIIPISKEIA ALILVQEQRV ADELDDGCVY VFPRKDCSPL KQDTFRVKLN ELAYEEKITD SNGEIFRFHA HAFRHTVGTR MINNGVPQHI VQKFLGHESP
EMTARYAHIF DETLKKEFTK FKETLVTNNG SILDLSEENT EADNTDLQWF KKNINAQALP NGYCRLPVIA GPCPHANACL DCTNFCTSKQ FLTEHEEHLE
RTKEILNRAK QNQWQRQVET NERVKNRLEQ IIHSLKETN
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| tnpC |
TnpC |
Tn558 |
366 |
3141-3506 |
+ |
| Class: | Accessory Gene |
| Sub Class: | Helper |
| Sequence Family: | Tn554_family |
| Comment: | target specificity and orientation in Tn554 family |
Protein Sequence:
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MIRKGNTTAI VQLAKDKSEK TRIRVEKTIS EMALKEEKIN FNSVAQKANV SKSWLYKQKD IRTRVETLRG MQISELTPRK PSKSPRSEDV LIKTLKSRIK
ALEEENERLK DQVQKLHGKL F
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| fla |
Fla |
Tn558 |
417 |
3789-4205 |
- |
| Class: | Passenger Gene |
| Sub Class: | Other |
| Sequence Family: | flavodoxin |
Protein Sequence:
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MKTLVIVSHP DMPNSRINKV WVEKAASYSN EITIHDLYRE YPDFIINVKR EQELVENHDN IIFQFPLYWY SSPSLLKKWI DEVIIYGWAY GSKGKRIFYN
RKLGLAISAG VKKGEFTSMG KNKHTLTQML TPFKSLCA
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| fexA (ARO:3002704) |
FexA |
Tn558 |
1428 |
4383-5810 |
- |
| Class: | Passenger Gene |
| Sub Class: | Antibiotic Resistance |
| Function: | antibiotic efflux (ARO:0010000) |
| Target: | phenicol antibiotic (ARO:3000387) |
| Sequence Family: | major facilitator superfamily (MFS) antibiotic efflux pump (ARO:0010002) |
| Comment: | perfect match to reference sequence for ARO:3002704 |
Protein Sequence:
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MKKDSKSKEM IQSEKRGSTR LLMMVLSLSV LVGAITADLV NPVLPLISKD LEASKSQVSW IVSGIALVLA IGVPIYGRIS DFFELRKLYI FAIMILASGS
LLCAIAPNLP LLVLGRMVQG AGMSAIPVLS IIAISKVFPQ GKRGGALGII AGSIGVGTAA GPIFGGVVGQ YLGWNALFWF TFLLAIMIVI GAYYALPTIK
PAESVGSNKN FDFIGGLFLG LTVGLLLFGI TQGETSGFSS FSSLTSLIGS VVALVGFIWR IVTAENPFVP PVLFNNKDYV NTVIIAFFSM FAYFAVLVFV
PLLVVEVNGL SSGQAGMILL PGGVAVAILS PFVGRLSDRF GDKRLIITGM TLMGLSTLFL STYASGASPL LVSVGVLGVG IAFAFTNSPA NNAAVSALDA
DKVGVGMGIF QGALYLGAGT GAGMIGALLS ARRDATEPIN PLYILDAMSY SDAFLAATGA ILIALIAGLG LKKRG
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| References |
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Kehrenberg C, Schwarz S. Florfenicol-chloramphenicol exporter gene fexA is part of the novel transposon Tn558. Antimicrob Agents Chemother. 2005 Feb;49(2):813-5. doi: 10.1128/AAC.49.2.813-815.2005. PubMed ID: 15673776
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