ISPpa6

  • Family IS5
  • Group IS427
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
EU909900 Y Paracoccus pantotrophus
Paracoccus pantotrophus DSM 11073
DNA section
IS Length : 850 bp

Ends


IR Length : 12/15

IRL : GGGTGTGTTGACAAAAAGGATTCCCCTGCGCGGTCGGCTGTGATTCAAGC
IRR : GGTCATGTTGACAAATGGCGAAGCCAGAGCCTGATGCAGGCGATATCGAT

Insertion site


Left flankDirect repeatRight flankDR Length
TTCTCAAAGTTAGCGTTGAAGA2

DNA sequence

GGGTGTGTTGACAAAAAGGATTCCCCTGCGCGGTCGGCTGTGATTCAAGCTCATCTCTACATGGGGATGAGCTTGGCACGCAACCTGATGTCCGACGACG
AATGGGCATTCTTTGAGGGCTTCATCCGAGCGGCTCGGCATCCGAACGGGCGCAAGCCTACGGACCATCGACTTGTTCTGGATGGTATTTTCTGGGTCGC
GCGGACCGGTGCGCCCTGGCGGGACCTGCCAGAGGAGTTTGGCAAGTGGTCATCGGTCTATCGGCAGTTCCGGCGCTGGACGCTCGCCGGGCTGTGGGAG
GACATCCTGGATGTCTTGAACCACGCGAAGCTTGCGCCCGACAAGCTCCAGATGATCGACAGCACCGTGATCAGGGCCCACCACCATGCGGCGGGCGCAA
AAGGGGGGCTCCGAAAGAGGCTCTTGGCCGTTCAAGAGGTGGGTTCTCGACCAAAATCCATCTCCGCGTTAACGGCGCTGGCCTCCCGATGAGGACCGAG
ATCACGCCCGGGCAGCATTCAGACTACACGGGCTATGATCTGGTGATGGCCGACAACCTGCCGCAGCCCGCCGTGTTGGTCGCCGACAGGGGTTATGACG
CTGATAAAATTCGAGAAGACATCGAGAGCCGTAACGCGCTGCCCATGATCCCGATGCGAAAGAACCGCAGGGTGCGCAAGGTGGTCGACATGACGATCTA
TACCCTGCGCAACATGGTCGAGCGGTGCTTCAACAAACTCAAGAACAGTCGCCGCTTGGCAACCCGCTACGACAAAACCGCAGACAGTTTCCTCGGCTTC
ATCGATATCGCCTGCATCAGGCTCTGGCTTCGCCATTTGTCAACATGACC
Recoding section
  • Recoding by frameshift
  • Frame
  • Type
  • Experimentally demonstrated

Stimulators :

  • Shine-Dalgarno sequence :
  • Secondary structure :

Recoding motif :

Protein section
ORF number : 3

 

ORF 1
LengthBeginEndStrandFusion ORF
432 bp143 aa61492+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MGMSLARNLMSDDEWAFFEGFIRAARHPNGRKPTDHRLVLDGIFWVARTGAPWRDLPEEFGKWSSVYRQFRRWTLAGLWEDILDVLNHAKLAPDKLQMID
STVIRAHHHAAGAKGGLRKRLLAVQEVGSRPKSISALTALASR

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
657 bp218 aa192848+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

LGRADRCALAGPARGVWQVVIGLSAVPALDARRAVGGHPGCLEPREACARQAPDDRQHRDQGPPPCGGRKRGAPKEALGRSRGGFSTKIHLRVNGAGLPM
RTEITPGQHSDYTGYDLVMADNLPQPAVLVADRGYDADKIREDIESRNALPMIPMRKNRRVRKVVDMTIYTLRNMVERCFNKLKNSRRLATRYDKTADSF
LGFIDIACIRLWLRHLST

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
788 bp262 aa61848+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MGMSLARNLMSDDEWAFFEGFIRAARHPNGRKPTDHRLVLDGIFWVARTGAPWRDLPEEFGKWSSVYRQFRRWTLAGLWEDILDVLNHAKLAPDKLQMID
STVIRAHHHAAGAKRGAPKEALGRSRGGFSTKIHLRVNGAGLPMRTEITPGQHSDYTGYDLVMADNLPQPAVLVADRGYDADKIREDIESRNALPMIPMR
KNRRVRKVVDMTIYTLRNMVERCFNKLKNSRRLATRYDKTADSFLGFIDIACIRLWLRHLST

 

Blast result :
Comments
ISPpa6 (orfAB) is 96% aa sililar to ISPaes1.
The third ORF is a putative ORFAB transposase reconstructed in silico by a possible -1 frameshift.
ISPpa6 has been identified by its transposition into entrapment vector pMEC1 (cI-tetA cassette).
At position 390, ISPpa6 contains a sequence 5'-AAAAG-3' that might function as a -1 translational frameshifting site.
References
1] Dziewit, L., Baj, J., Szuplewska, M., Maj A., Tabin, M., Czyzkowska, A., Skrzypczyk, G., Adamczuk, M., Sitarek, T., Stawinski, P., Tudek, A., Wanasz, K., Wardal, E., Piechucka, E., Bartosik, D. (2012) PLoS ONE 7: e32277