TnShfr1

  • Family Tn3
  • Group
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
NC_008345 ND Shewanella frigidimarina
Shewanella frigidimarina NCBM4000
DNA section
IS Length : 5131 bp

Ends


IR Length : 39/41

IRL : GGGGTCGTCTCAGAAAACGGAAAAAATCGTACGCTAAGACCGGTTTGGCT
IRR : GGGGTCACCTCAGAAAACGGAAAAAATCGTACGCTAAGACCCAGAGAGCG

Insertion site


Left flankDirect repeatRight flankDR Length
GGTTATTGCCTATCAAAACTACTAT5

DNA sequence

GGGGTCGTCTCAGAAAACGGAAAAAATCGTACGCTAAGACCGGTTTGGCTAGCCGGGTAGTAGGAGTCCCATTAGTCACGCCTGCCGGGCTGCGGCTTGG
TCTGGTTGAGAACTCGGTTCTTTGTGGCGATGATCCACGAAGTTGCACCCATCGACGCTGTGTTCACAGGCAACAATCTCCAGTTGCAGCGTCGTATGGA
AGATGCTGAATCGGTCAGCCAGCAACAACTTGAGGGTTTTGAGCAACTCGTCGGGCCCTATTTCCGGCGCATACACGATATGAGCGGTCATGCTGACCTT
GCCGCTCGTGAGCGCCCATACGTGCAAGTCATGCAGCCCTGTCACGCCTGGCACGGCCTGAACAGATGCCATCAAGGCTCCCATGTCAATGCCGTCTGGG
ACTCCCTCCAGCAAGACATTCAGGCTTTCCTTGAGTAGCAGCCAAGTTCGTGGCAGCACCCATAGCCCGATTGCCACGGCGACGACCGCATCTACCCACA
CCCAGCCGGTGAATCGGATGACCAGCGCAGCTCCGATCACGCCGATGGAGCCAATCATGTCGCTCCAGACCTCCAGATAAGCGCCTTTGACGTTGAGGCT
CTTGTCCTTGCCGCCCTGAAGCATACGCATGCTGATGAGGTTGACGATCAGACCCAGCACTGCTACCACCAGCATCCCGCTGGACTGAACCTGCGCTGGC
TCGCGCAAACGCTGCCAGCCCTCATACAGGATGTAGCCAGCGACGCCGAAGAGCAACAGGGCGTTGAATGCGGCCGCAAGGATTTCGAAGCGGTAGTAGC
CATAGGTGCGCTTGGCATCGGCTGGCCGTCTCGCCACCCGTACAGCCGCCAAGGCGATGGCCAGCGCCGCTGCATCCGTGAACATGTGCGCCGCATCTGA
GAGCAGGGCCAGGCTGTTGAAAACGATGCCTGCGGCGACTTCGGCCAGCAAGAAGCTCCCGGTCAGCGCCAGGGCGATCCAGAGCGATTTTTCATTGCGC
TCGCTGGGTAGGGCATGGGTGTGACCGGTGCTCATTTTCGTCCTTCTTCTGAGTTCATTTTTGTTCAGCGTGACCGGAAGCCGGCACCCAGCGATACAAC
GTCGGGATTGAGACCCCGAGGTTCTTGGCCACGTCCTTGGGAGCGATCCCGCTGGCGAGCAGCTTCTTGGCCGATTCAATCTTGCTTTTGGTCATCTTCG
GTTTGCGCCCTCCCTTGCGGCCTGACAGCCGGGCGACCGCCAATCCTGCTCGGGTCCGCTCCACCGTCAGCTCGCGCTCCATTTCGGCGAGGCTGGCCAT
GACGTGAAAGAAGAACCGTCCCGACGGCGTGCCGGTGTCGATGGCGTCGGTGAGACTCTTGAACTGGATGCTCTGCTTGTGCAACTCGCTGACCAGATCG
ACCAATTGCTTGACGCTGCGGCCCAGGCGATCCAGCTTCCAGACGACCAGCGTGTCTCCCTTGCGTAGCATTTCAAGCGCCTTGGCCAAGCCGGGGCGCT
CGGCTCTCGTGCCGCTTAATTTGTCCTCAAAGAGCTTTTGGCACCCGGCCTGGGTCAAGGCCTCCCGCTGTAGCTCCAGGTTCTGATCCTGCGTCGAGAC
GCGCGCATAGCCAACCAGCATGGCACGGTCAGACCGCTGCCTTGCCGCACTGAGCGCAAAACTTCGCACCCGGTTGCAGTGTGGTTCCACATTGCGCGCA
AGCCGAAGGAACCAACGAAGTCCCGCACTGCTGGCAGAAGCGAGCGCCTGGCGCGTTAGATGCCTTGCAGTTGGGGCAAGCAAGGCCGCCATTACCCCAC
CCGCCCGCTGGAGGCCCGCCGCTTCCGTACCCACCGCCACCACCGTGATGCCCACCACCGCTGTAACCACCACCGTGGTGGCCACCGAAAAGTCTGTCAA
AAATACCCATGAGTCTTTCTCCTTTCGTAAACACGTCAAAGCCACTTGGGGCAGCGGTTGGCTACATCCCTATTTCTCGAAACGCGTTGATATGATAAGA
ATTCAAGAATAAAGTTTCAAGAACTGTTTTCGAGAATCGCAACGCATTGATTTGCTGTACCGCGCCAGAGGGTTGAGCGGGATTGTCGCAAACCTACGTT
TTTGAGAAGAAGGAGACTGCATGCCCCGCCGTTCAATCCTCTCCGCCGCAGAGCGCGACAGTCTCTTGGCGTTGCCCGATACCCAAGACGAACTCATCCG
GCTCTACACGTTCAGCGAACCCGACCTGTCACTAATCCGCCAGCGGCGCGGTGACGCCAACCGCCTGGGTGTCGCGGTGCAATTATGCTTATTGCGCTTT
CCCGGTCAGGGCCTGCTGCCCGACGCTGCGGTGCCGATGCCCCTGCTGCAATGGATCGGACGGCAACTGCGCATCGATCCATCGTGCTGGCCACAGTATG
CAGAGAGGGAAGAAACCCGGCGCGAGCATCTGCTTGAGCTGCGTGCATATTTGGGCATGGAGCCGTTCGGCCTGGCGCACTATCGGCAGGCTGTCCATGC
CGCGACCGAGTTGGCCTTGCAAACCGACAAGGGCATCATGCTGGCCAACAGTGTTCTCGACGACCTGCGGCACCGACACGTCATCTTGCCGACGCTGGAT
GTTGTCGAGCGCGTCTGTGCCGAGGCGATCACCCGCGCCAACCGGCAAATCTACGAAACCTTGTCCGAACCGCTATCGGACGCGCATCGTCGCCGCCTTG
ACGATCTGCTCAAACGCCGGGACAACGGCAAAACGACCTGGCTGGCCTGGCTGCGCCAGTCACCCGTCAAGCCCAATTCGCGGCACATGCTCGAACACAT
CGAACGCCTCAAGGCATGGCAGGCGCTCGACCTGCCTTCCGGCGTCGAGCGGTCGGTGCACCAGAATCGCCTGCTCAAGATCGCCCGCGAGGGTGGCCAG
ATGACACCCGCCGACCTGGCCAAGTTCGAGGCGCAGCGGCGCTACGCCACCCTGGTCGCGCTCGCCATCGAGGGTATGCAGGTATGGCCACCGTCACCGA
TGAAATCATCGACCTGCATGATCGAATCCTGGGCAAGCTGTTCAACGCCGCCAAGAACAAGCATCAGCAGCAGTTCCAGGCATCCGGCAAGGCGATCAAC
GCCAAGGTGCGGCTGTTTGGGCGCATCGGTCAGGCGCTGATCGAGGCCAAGCAAGCGGGCCGCGATCCGTTCGCCGCAATCGAGGGCGTACTATCCTGGG
ATGCTTTCGCCGAAAATGTCACCGAAGCGCAGAAGCTCGCGCAGCCCGAGGACTTCGATTTCCTGCACCGCATCGGCGAGAGCTACGCCACGTTACGCCG
GTACGCGCCGGAATTCCTCGCCGTGCTCAAGCTGCGGGCTGCGCCCGCTGCCAAGGATGTGCTGGACGCCATCGAGGTGCTGCGCGGCATGAACAGCGAC
AACGCACGCAAGGTGCCTGCCGATGCGCCGACCGACTTCATCAAGCCGCGCTGGCAGAAGCTGGTGATGACCGATGCCGGCATCGACCGGCGCTACTACG
AGTTGTGCGCACTGTCGGAACTGAAGAACGCGCTGCGCTCCGGCGACATCTGGGTGCAAGGCTCACGCCAGTTCAAGGATTTCGAGGACTACCTGGTACC
GCCTGTGAAATTCGCCAGCCTCAAGCTGGCCAGCGAACTGCCGCTGGCTGTGGTCACCAACTGCGACCAGTACCTGCATGACCGGCTGACGCTGCTAGAA
ACACAGCTTGCGACCGTCAACCGCATGGCGGCGGCCAACGACCTGCCGGACGCCATCATCACCGAGTCTGGCCTGAAGATCACGCCTCTGGATGCGGCGG
TGCCTGACACCGCGCAGGCGCTGATCGACCAGACCGCGATGATCCTGCCGCACATCAAGATCACCGAACTGCTTATGGAAGTGGATGAATGGACGGGCTT
CACCCGCCACTTTACGCACCTGAAATCGGGCGACCTGGCCAAGGACAAGAACCTGCTGCTGACCACCATACTGGCCGACGCGATCAATCTCGGCCTGACC
AAGATGGCCGAGTCCTGTCCCGGCACAACGTATGCCAAGCTCGCCTGGCTACAAGCCTGGCATACCCGCGATGAAACCTATTCGACGGCGCTGGCCGAAT
TGGTGAACGCGCAGTTCCGGCATCCCTTCGCCGAGCATTGGGGTGACGGCACCACGTCATCGTCGGACGGCCAGAACTTCCGCACCGGCAGCAAGGCCGA
GAGCACCGGGCACATCAACCCGAAATATGGCAGCAGCCCAGGGCGGACGTTTTACACGCACATCTCCGACCAGTACGCGCCGTTCCACACCAAGGTCGTG
AACGTCGGCGTGCGCGACTCGACCTACGTGCTCGACGGCCTGCTGTACCACGAGTCCGACCTGCGCATCGAGGAGCACTACACCGACACGGCGGGCTTCA
CCGATCATGTCTTTGCCCTCATGCATCTGCTGGGCTTCCGCTTCGCGCCGCGCATCCGCGCCCTGGGCGACACCAAGCTGTTCATCCCTAAGGGTGAAGC
CAGTTACGACGCACTCAGACCGACGATTAGCAGCGACAAGTTGAACATCAAGGCTATTCGTGCCCATTGGGATGAAATCCTGCGCCTGGCTACCTCGATC
AAACAGGGCACGGTGACGGCCTCGCTGATGTTGCGCAAGCTCGGCAGCTACCCGCGCCAGAACGGCCTGGCCGTTGCGCTGCGCGAGCTGGGGCGCATCG
AGCGCACGCTGTTCATCTTGGACTGGCTGCAAAGCGTGGAACTACGCCGTCGTGTGCATGCCGGATTGAACAAGGGCGAAGCCCGCAATGCGCTGGCCAG
GGCGGTGTTCTTCAACCGGCTGGGCGAAATCCGCGACCGCAGTTTCGAGCAGCAGCGCTACCGGGCCAGTGGCCTCAACCTGGTGACGGCGGCCATCGTG
CTGTGGAACACGGTCTACCTGGAGCGCGCCGCGAATGCTTTGCGCGGCCACGGCCATGGTGTCGATGAAGGGCTGTTGCAGTACCTGTCGCCGCTGGGTT
GGGAGCATATCAACCTGACCGGCGATTACCTCTGGCGCAGTAGCTCCAAAGTAGGCGTGGGGAAATTCCGACCGCTACGTCCGCTCTCTGGGTCTTAGCG
TACGATTTTTTCCGTTTTCTGAGGTGACCCC
Protein section
ORF number : 4

 

ORF 1
LengthBeginEndStrandFusion ORF
960 bp319 aa103576-No
ORF function : Passenger Gene
Annotation : cation efflux pumpDescription :

ORF sequence :

MSTGHTHALPSERNEKSLWIALALTGSFLLAEVAAGIVFNSLALLSDAAHMFTDAAALAIALAAVRVARRPADAKRTYGYYRFEILAAAFNALLLFGVAG
YILYEGWQRLREPAQVQSSGMLVVAVLGLIVNLISMRMLQGGKDKSLNVKGAYLEVWSDMIGSIGVIGAALVIRFTGWVWVDAVVAVAIGLWVLPRTWLL
LKESLNVLLEGVPDGIDMGALMASVQAVPGVTGLHDLHVWALTSGKVSMTAHIVYAPEIGPDELLKTLKLLLADRFSIFHTTLQLEIVACEHSVDGCNFV
DHRHKEPSSQPDQAAARQA

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
567 bp188 aa16211055-No
ORF function : Accessory Gene
AG : Tn3 resolvase

ORF sequence :

MLVGYARVSTQDQNLELQREALTQAGCQKLFEDKLSGTRAERPGLAKALEMLRKGDTLVVWKLDRLGRSVKQLVDLVSELHKQSIQFKSLTDAIDTGTPS
GRFFFHVMASLAEMERELTVERTRAGLAVARLSGRKGGRKPKMTKSKIESAKKLLASGIAPKDVAKNLGVSIPTLYRWVPASGHAEQK

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
282 bp93 aa19101629-No
ORF function : Passenger Gene
Annotation : conserved hypothetical proteinDescription :

ORF sequence :

MGIFDRLFGGHHGGGYSGGGHHGGGGGYGSGGPPAGGWGNGGLACPNCKASNAPGARFCQQCGTSLVPSACAQCGTTLQPGAKFCAQCGKAAV

 

Blast result :
ORF 4
LengthBeginEndStrandFusion ORF
2978 bp989 aa21215098+No
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MPRRSILSAAERDSLLALPDTQDELIRLYTFSEPDLSLIRQRRGDANRLGVAVQLCLLRFPGQGLLPDAAVPMPLLQWIGRQLRIDPSCWPQYAEREETR
REHLLELRAYLGMEPFGLAHYRQAVHAATELALQTDKGIMLANSVLDDLRHRHVILPTLDVVERVCAEAITRANRQIYETLSEPLSDAHRRRLDDLLKRR
DNGKTTWLAWLRQSPVKPNSRHMLEHIERLKAWQALDLPSGVERSVHQNRLLKIAREGGQMTPADLAKFEAQRRYATLVALAIEGMATVTDEIIDLHDRI
LGKLFNAAKNKHQQQFQASGKAINAKVRLFGRIGQALIEAKQAGRDPFAAIEGVLSWDAFAENVTEAQKLAQPEDFDFLHRIGESYATLRRYAPEFLAVL
KLRAAPAAKDVLDAIEVLRGMNSDNARKVPADAPTDFIKPRWQKLVMTDAGIDRRYYELCALSELKNALRSGDIWVQGSRQFKDFEDYLVPPVKFASLKL
ASELPLAVVTNCDQYLHDRLTLLETQLATVNRMAAANDLPDAIITESGLKITPLDAAVPDTAQALIDQTAMILPHIKITELLMEVDEWTGFTRHFTHLKS
GDLAKDKNLLLTTILADAINLGLTKMAESCPGTTYAKLAWLQAWHTRDETYSTALAELVNAQFRHPFAEHWGDGTTSSSDGQNFRTGSKAESTGHINPKY
GSSPGRTFYTHISDQYAPFHTKVVNVGVRDSTYVLDGLLYHESDLRIEEHYTDTAGFTDHVFALMHLLGFRFAPRIRALGDTKLFIPKGEASYDALRPTI
SSDKLNIKAIRAHWDEILRLATSIKQGTVTASLMLRKLGSYPRQNGLAVALRELGRIERTLFILDWLQSVELRRRVHAGLNKGEARNALARAVFFNRLGE
IRDRSFEQQRYRASGLNLVTAAIVLWNTVYLERAANALRGHGHGVDEGLLQYLSPLGWEHINLTGDYLWRSSSKVGVGKFRPLRPLSGS

 

Blast result :
Comments
A single copy of TnShfr1 is encoded by Shewanella frigidimarina. This is a transposon and encodes the transposase (ORF4) , resolvase (ORF2), a cation efflux pump (ORF1), and a small conserved hypothetical protein (ORF3).
The TnShfr1 transposase is 92% aa similar to TnSod9.
References
1] Romine, M. F. (2008) Direct submission