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Terminal Inverted Repeats | |
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Recombination Sites | |
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Internal Transposable Elements | |
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Internal Repeats | |
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References | |
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| Name: Tn558.3 |
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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: | Bacillus sp. HBCD-sjtu | Molecular Source: | chromosome |
| Place of Origin: | Shanghai, China | Date of Isolation: | 2017 |
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| Map |
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| Sequence |
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--------10 --------20 --------30 --------40 --------50 --------60 --------70 --------80 --------90 -------100
TTAAACATAG TATCCTAAAC TAGAGTACTC TAAGTACTCG AAGTTTAGGA TTTTTTAATT ACAGTGCTTT AACTATTAAA TATATAAGGG TATTATTAAT 100
AGTAGTTAAA GTATTTAAAG GTGGTGGAAA GATGAAGGTT CAGAAAGTAA TTGTGGAGGA AAAATCATAT CCGTTATACA TACTGCTAGA TAAAGAATTT 200
GAAGTGATAG AACCGGTTAA GCGATTTATA AAGTACTTGG ATAATACGGG CAAAGCTCCA AATACCATTA AAACATATTG TTATCATCTC AAGCTGTTTT 300
ATGAATTTAT GAGCCAAAGT AGAATCGAAT TAGGAGATTT ACAATTTGAG GATTTAGCAA ACTTTGTAGG ATGGTTAAGA AATCCAGCAG GGCATTTAAA 400
GGTAATAGAT ATACAACCAA AGAAGGCTAA AAGAGAGGAA ACATCAGTTA ATTCCATACT TAACGCTGTA ACTAGTTTCT TAGAGTATTT AAATCGCACA 500
GAAAATTTTA AAGCTATAGA TATGTCTAAA GAAGCAAGAG GAAGAAACTT TAAGGGGTTT CTTCACCATA TTTCTAAAGG TAGATCCTAT AAAAAAAATA 600
TTTTAAAGCT TAGGGTCAAA AAGAAACTTG TACAAGTATT AGAACATGGA CAAGTCAAAG CAATAATTGA GGCATGTCAT ACCAAAAGAG ATAAGTTACT 700
TATTATGCTT ATGTATGAAG GGGGACTTCG GATAGGAGAA GCATTATCCC TTCGTATTGA AGATATTTCA ACATGGGATA ACCAGATTAA CATCAGGCCA 800
AGAGATCATA ATGAAAATGG AGCTTATATT AAACTTAAAA AAGAAAGAAC TATTGATGTA AGTAAGGAAT TAATGGCATT ATATACCGAT TACTTAGTAC 900
ATGAATATGG GGAAGATTTA GATCATGATT ATATATTTAT TAATCTTAAA GATTCTTATT TTGGCCACCC TCTAAAATAT CAAAGTGTAT TAGACTTAAT 1000
AAGAAGACTA GGAAAACGGA CAGGGATTAC TTTCACTGCC CATATATTAC GTCATACGCA TGCCACAGAG CTTATTAGAA GTGGATGGGA TGCTGCATAT 1100
GTACAAAAAA GATTAGGGCA TGCCCATGTA CAAACAACAC TTGATACGTA TGTTCATCTT TCTGATCAAG ATATGAAGAA TGAATATAAA AAGTATCTTC 1200
AAGGGAGAGA AACATGACAA TGAAATTTCC AAGTGTAGCA ACTAATCGAA AGCTTATCGC TAGTACAGAG ATTAATAAAA AAATAGCTAA TATGACAAGT 1300
GTTTTAAAAG GTTATTGGGC AGCAGATAGA TGGGATATAA GAATTTGTCC GCATCCTAGT GCAATTGAGT TAAGTAAGAA TCCGTCACTA AGAAATCGTT 1400
GGGTAAATTT CGATAAGGTG GAAAATGTCT GGTTGAAAAC AGAATTAAAA TATTTTTATT ACCTTCACTT GAATAATGGA GCTTGGAATG CAAAATCCGT 1500
TTGGATTAGA AAGGGAACAG TGATAAGCCG GATGATGGGA TTTTTAAATT TAAAATATCC TAATATTACA TCGATAACCG AAGTGCCTAT AAAAAAAGCT 1600
TTGACAGAAT ACCGGACCTA CTTAACAGAA CAAAAAGTAA AAACTACGAC TACTAATTAC AAACTTGATG TAAATCAGCA GAAAGTTACT GTACATGCGA 1700
ATTCCTATTA CGTTACTCAT CTTAAGCAGT TTATGGAATT CTATGAGGAC TTCTATTTTG ATGGGGAAGA ATGGGAAAAA GATGTTTGGA ATCGAAGAAA 1800
ATTATCATTA CCGGAAGATA AGGTAAACCC AACATCCTAC GAATATACGA TCAACTTTAA GGGTTTTAAG AATAATTATT TTAAAGAAAT AGTTAAGCGA 1900
TATTGTAAAC TAATGTTAAA CACAGCTAGC TTTTCTCACG TAGTAGATAT AGCTTCAAAA TTAAAAGAAT TTTTTAATTT CATGAACAAA AATTGTGAAG 2000
GTATACAAAG GATTCATCAA TTAACTAGAA ATGAAATTGA GCAATATTTT AATTATATTA ATTTAAAAGG TTTAAAACCC AGTACTGTAA CTGGACGAAT 2100
ATCTACTTTA GACGTTTTTT TTACTACAAT TCAAAGATAT GACTGGAAGG ATACACCTTC TAAGATCCTT ATCTTTCAAG AAGATTACCC TAAAGTGCCG 2200
AAGGCACTAC CACGTTATAT TGATGAACAT ATACTTGAAC AATTAAATGG GAAATTAGAT AAATTGGAAC CTTATATTGC TACAATGGTT ATGGTACTTC 2300
AAGAATGCGG GATGCGTATC AGTGAACTTT GTACATTGAA AAAAGGGAGC GTCATAACCG ATAAAGAAGG GGATTGCTTT TTAAAGTATT ATCAGTGGAA 2400
AATGAAGAAA GAGCATATCA TTCCTATTTC TAAAGAAATT GCTGCATTGA TATTAGTTCA AGAGCAAAGG GTGGCTGATG AACTCGATGA TGGATGTGTA 2500
TATGTGTTTC CCCGAAAAGA TTGCTCACCA TTGAAACAAG ATACCTTTAG GGTTAAATTA AATGAACTAG CTTATGAAGA AAAGATAACG GACAGCAACG 2600
GAGAAATTTT TCGTTTTCAT GCTCATGCCT TTCGGCATAC AGTTGGCACT AGAATGATAA ATAACGGAGT GCCACAACAT ATTGTCCAGA AGTTCTTGGG 2700
TCACGAATCA CCGGAAATGA CGGCAAGATA TGCACATATT TTTGATGAAA CCCTAAAGAA GGAATTTACG AAATTTAAGG AAACCTTAGT AACGAATAAC 2800
GGTAGCATTC TGGATTTAAG TGAGGAAAAT ACTGAAGCTG ACAATACAGA TCTTCAATGG TTTAAAAAGA ATATCAATGC ACAGGCACTT CCTAATGGCT 2900
ATTGTCGGTT ACCAGTAATT GCAGGACCAT GTCCTCACGC AAATGCATGT TTAGATTGTA CGAATTTCTG TACAAGTAAA CAATTTCTTA CTGAACATGA 3000
AGAGCACTTA GAGCGAACTA AAGAAATACT AAATAGGGCT AAACAAAACC AATGGCAGCG TCAGGTTGAA ACCAATGAAC GTGTTAAAAA TAGATTAGAA 3100
CAGATTATTC ATTCGTTAAA GGAGACGAAT TAAAATGATT AGAAAAGGTA ACACAACTGC CATAGTTCAG CTAGCTAAAG ACAAGTCGGA GAAAACAAGA 3200
ATTAGGGTTG AAAAGACAAT TTCAGAGATG GCATTGAAAG AAGAGAAGAT TAATTTTAAT TCCGTTGCAC AAAAAGCAAA TGTTTCAAAG TCATGGCTTT 3300
ACAAACAAAA AGATATTAGA ACTAGAGTGG AGACATTAAG AGGGATGCAG ATAAGTGAGT TAACCCCCCG TAAACCTAGT AAAAGCCCTC GTTCAGAGGA 3400
CGTATTAATA AAAACCTTAA AAAGCCGTAT AAAGGCGTTA GAAGAAGAGA ATGAACGGTT AAAGGATCAA GTTCAAAAAT TACATGGCAA GCTGTTTTAG 3500
CAGATTTGTG TTTCTTGGAA TTTATTGGGC ACTTTGAATT GGCTACCTAA AATGAAATCG CTAAAACCTT CAATAACTTC AATAGCCCAT TTCCCTAAAT 3600
GTGTTAAGGG GAAATGGGCT TTCTTCTAGT ATTGTTGGCA TGATCGCAGA AGTGTTTTAT GCTCTTAAAT AATACTTTTT AATATATTGC AAATACTCAT 3700
TAGCACTTTT CTGTATCTCT TCGCCCTTCA TATCCGAATT AGCACCGTAA AGTACAAACT CTGGTACATA TTCAGCATGA ATCTATGCAC ATAAAGATTT 3800
GAATGGTGTT AACATCTGGG TTAATGTATG CTTGTTTTTA CCCATACTTG TAAATTCACC TTTTTTTACG CCAGCTGATA TAGCTAATCC TAATTTTCGA 3900
TTATAAAATA TTCTTTTACC CTTTGATCCG TAAGCCCATC CATATATAAT CACTTCATCG ATCCATTTTT TTAATAATGA AGGAGAACTA TACCAATATA 4000
ATGGAAATTG AAAAATAATA TTATCATGAT TTTCAACTAA TTCCTGCTCT CTTTTTACAT TTATAATAAA ATCAGGATAC TCTCTATAAA GATCATGAAT 4100
GGTAATTTCG TTTGAATAAG ACGCTGCTTT TTCTACCCAA ACTTTATTGA TTCGAGAATT TGGCATATCT GGGTGAGAAA CGATCACCAA TGTTTTCATT 4200
GTTTCATCCT TAACATACTC AACTTTCGCA CCAATAAAAC AGTGTACGAA AGTTGAGTTA CTTAAAAGTA TTCTATTCTA AGAAATTCAA ATTTGCGTGA 4300
TTCCTAAGCT ATTTATTTAC AGCTTAAACT ATAGAAGATG AACTAAACAA TAACTAATCT TTACATAACT AAGTTATTAC CCACGCTTTT TTAAACCTAA 4400
TCCAGCTATT AAGGCAATGA GTATTGCCCC TGTAGCTGCA AGGAACGCAT CTGAGTAGGA CATAGCGTCC AATATATATA ATGGATTTAT CGGCTCAGTA 4500
GCATCACGTC GAGCGGATAA TAATGCTCCA ATCATACCTG CTCCAGTTCC TGCTCCAAGG TACAAAGCAC CTTGGAAAAT CCCCATTCCG ACACCAACCT 4600
TGTCTGCATC GAGTGCACTT ACTGCGGCGT TATTTGCGGG AGAATTCGTG AATGCAAAAG CAATCCCTAC TCCGAGGACC CCCACGGAAA CTAACAGAGG 4700
TGAAGCACCA GATGCATAGG TGGACAAGAA TAAGGTAGAC AGCCCCATCA GAGTCATCCC AGTAATTATC AGACGTTTAT CCCCAAATCG ATCAGAAAGA 4800
CGGCCAACGA AGGGAGATAA GATTGCAACA GCCACACCAC CTGGCAACAA TATCATTCCA GCCTGTCCAG AAGAGAGTCC ATTCACCTCA ACGACTAGTA 4900
ATGGGACGAA CACAAGAACA GCGAAATAAG CAAACATCGA AAAAAATGCA ATTATGACCG TATTGACATA ATCCTTGTTA TTGAACAGGA CAGGTGGTAC 5000
AAATGGATTT TCTGCGGTAA CAATTCTCCA AATAAATCCC ACCAAAGCTA CAACAGAACC AATTAGGCTA GTTAACGATG AGAACGAAGA AAAACCAGAA 5100
GTTTCTCCTT GAGTGATGCC AAAAAGGAGT AATCCTACTG TGAGGCCGAG GAATAAACCA CCAATGAAAT CAAAGTTCTT ATTGCTTCCT ACGGATTCTG 5200
CCGGTTTAAT TGTCGGTAAC GCGTAGTAGG CACCAATAAC AATCATAATG GCTAACAAAA ATGTGAACCA AAACAAGGCA TTCCACCCTA AATATTGACC 5300
AACTACTCCA CCAAATATTG GACCAGCAGC AGTTCCAACA CCAATACTTC CTGCGATAAT TCCCAAAGCT CCCCCACGTT TTCCTTGTGG GAAAACCTTC 5400
GAAATTGCAA TGACTGATAG AACTGGAATT GCGGACATCC CAGCACCCTG AACCATTCTT CCCAAAACCA ACAATGGGAG GTTCGGGGCA ATTGCACATA 5500
AAAGACTACC ACTTGCCAGA ATCATAATGG CAAAGATATA TAGCTTTCGT AACTCAAAAA AGTCTGAGAT TCGACCATAA ATCGGAACTC CAATCGCAAG 5600
AACAAGTGCA ATACCACTAA CTATCCAACT CACTTGAGAT TTCGAAGCTT CTAAATCTTT GCTTATTAGT GGAAGTACGG GATTGACTAA ATCAACCGTA 5700
ATTGCAGCTA CAAGTACAGA TAGGGAGAGT ACCATCATTA AAAGCCTAGT AGAACCCCTT TTTTCAGATT GAATCATTTC TTTAGATTTA CTATCCTTTT 5800
TCATTTTATT TCCTCCTAAA ATATATTGTG ATTTTAGGAG GCTAAATCCA CTGCTTTCAC CATAAACCTC ACCTCATATC TATTTATATT GTAAAACCAA 5900
ATCAACGAAC TCACCATATT TCTACAGCAT GATTAAAGAT TCGGTTCTCC AAACTAACTG AACTGATCAA ACAAAAAAAA GGCACCAGTT TAACAACCGG 6000
TGCCTAATCA TTCGTATGCA TTTTTACAAA TGCAATAGAT TCATAAATTT TTGCCCATTA TATAAAAGGA GGCAAAAAGT TTTCCGGTAG TGTTTCCATT 6100
TTTTGTTTTT GTGAAAAAGG ACATACTGAT CCCGTTGTAC CTAAATCCCC TGAAACTTTT ACATGCTTTC TAAACTCGAC ATTAATGAAA TCAATTCCCA 6200
TTACTTTTTG CCTCCTTTCT CATATTGTGA TAATAACACA ATAATAATTG ATGAAAAAGA AATAATCAAC CCTACTTTTT TGAAAACCAA TTTAAAGCTT 6300
TACTACTTTT ACTTACATAA TAAAGGCAGG TGCAGTATAA ACTTTTTTAA ATAGGTCTTC TTTAACGAGC AGGTAGCGTC AGTTAAAGTA GATAATTTAA 6400
GATCGAAATC ATATTATAGA TATTCCGAAA TTGGGCGTGA TTGTTGCAGG TCAAAAGCTT AATTCCTCGA TAAAATAAAA AGGAATTAGT TTTTTTATTT 6500
GTGGTACATT CTTCTGACCG TAATCAATTG TCATCTAATA ATTACATTGT ATTTTTTCAT TTGATTTAAC ACGTTAAATA TATGTTCTTA AAGTAAAAAC 6600
ATTGATGTTA ATGGATTTTT AGTAATTTAC TCTTGATAA
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| ORFs |
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| Gene Name |
Associated TE |
Coordinates |
Class |
Sub Class |
Orientation |
| tnpA |
Tn558.3 |
132-1217 |
Transposase |
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+ |
| tnpB |
Tn558.3 |
1214-3133 |
Transposase |
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+ |
| tnpC |
Tn558.3 |
3135-3500 |
Accessory Gene |
Helper |
+ |
| fla |
Tn558.3 |
3783-4199 |
Passenger Gene |
Other |
- |
| fexA (ARO:3002704) |
Tn558.3 |
4377-5804 |
Passenger Gene |
Antibiotic Resistance |
- |
| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| tnpA |
TnpA |
Tn558.3 |
1086 |
132-1217 |
+ |
| 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 AAYVQKRLGH AHVQTTLDTY VHLSDQDMKN EYKKYLQGRE T
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| tnpB |
TnpB |
Tn558.3 |
1920 |
1214-3133 |
+ |
| 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 |
Tn558.3 |
366 |
3135-3500 |
+ |
| 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 |
Tn558.3 |
417 |
3783-4199 |
- |
| 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 |
Tn558.3 |
1428 |
4377-5804 |
- |
| 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 LVAAITVDLV NPVLPLISKD LEASKSQVSW IVSGIALVLA IGVPIYGRIS DFFELRKLYI FAIMILASGS
LLCAIAPNLP LLVLGRMVQG AGMSAIPVLS VIAISKVFPQ 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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