ISPak1

  • Family IS5
  • Group IS427
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
GQ871938 Y Paracoccus alkenifer
Paracoccus alkenifer DSM 11593
DNA section
IS Length : 853 bp

Ends


IR Length : 13/15

IRL : GGGTCAGGACCCATTGATTTCAGCCGCGCGGCATGATTCAGGCTCCGCAA
IRR : GGGTCAGGACTCGTTCTCGATTCATAGCCAGAACATGACGGTTGCGGCGA

Insertion site


Left flankDirect repeatRight flankDR Length
CCGGAGATCCTAAAAATGCGGA2

DNA sequence

GGGTCAGGACCCATTGATTTCAGCCGCGCGGCATGATTCAGGCTCCGCAAGGAGGCTGGATCATGAGCAACCTTTTCTGGCTGACGGATGCGCAGATGGC
CCGCCTTCAGCCGTTTTTCCCGAAGAGCCACGGCAAGCCGCGCGTCGATGACCGGCGTGTTCTCAGCGGCATTATCTTCATCAATCGCAATGGCTTGCGG
TGGTGCGATGCGCCCAAGGAGTATGGTCCACCGAAGACCCTCTATAATCGTTGGAAGCGCTGGGGCGAGAAAGGCGTCTTCGCCCGGATGATGGAAGGCC
TGGCCTCCGAGGCGGCCGTTCCGAAGACGGTGATGATAGACGCGACCTATCTGAAGGCGCATCGCACGGCCTCCAGCCTGCGGGCGAAAAAAGGGGGCCC
GGCGACCAGAGGGGCCGCCTGATCGGCCGCACCAAAGGCGGCATGAACACCAAACTGCACGCCGTCACCGACGCTGATGGGCGGCCGATCCGGTTCTTCA
TGACTGCAGGTCAGGTGAGCGACTACAGCGGTGCTGCGGCCCTGTTGGGCAGCTTGCCGGCGGCAGAATGGCTGCTGGGCGACCGTGGCTATGATGCCGA
TTGGTTCAGAGATGCGTTGAAAGACAAGGGGATTAAGCCCTGCATACCGGGACGGAAGTCCCGTGGAAAACCCGTCAAGTATGACAAGCGCCGCTACAAA
CGCCGCAACCGGATCGAGATCATGTTCGGGCGGCTGAAGGACTGGCGACGGGTCGCAACCCGTTACGACAGATGCCCGAAGGTCTTCCTCTCAGCCATCG
CCCTCGCCGCAACCGTCATGTTCTGGCTATGAATCGAGAACGAGTCCTGACCC
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
390 bp129 aa33422+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MIQAPQGGWIMSNLFWLTDAQMARLQPFFPKSHGKPRVDDRRVLSGIIFINRNGLRWCDAPKEYGPPKTLYNRWKRWGEKGVFARMMEGLASEAAVPKTV
MIDATYLKAHRTASSLRAKKGGPATRGAA

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
582 bp193 aa251832+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

LEALGRERRLRPDDGRPGLRGGRSEDGDDRRDLSEGASHGLQPAGEKRGPGDQRGRLIGRTKGGMNTKLHAVTDADGRPIRFFMTAGQVSDYSGAAALLG
SLPAAEWLLGDRGYDADWFRDALKDKGIKPCIPGRKSRGKPVKYDKRRYKRRNRIEIMFGRLKDWRRVATRYDRCPKVFLSAIALAATVMFWL

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
800 bp266 aa33832+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MIQAPQGGWIMSNLFWLTDAQMARLQPFFPKSHGKPRVDDRRVLSGIIFINRNGLRWCDAPKEYGPPKTLYNRWKRWGEKGVFARMMEGLASEAAVPKTV
MIDATYLKAHRTASSLRAKKRGPGDQRGRLIGRTKGGMNTKLHAVTDADGRPIRFFMTAGQVSDYSGAAALLGSLPAAEWLLGDRGYDADWFRDALKDKG
IKPCIPGRKSRGKPVKYDKRRYKRRNRIEIMFGRLKDWRRVATRYDRCPKVFLSAIALAATVMFWL

 

Blast result :
Comments
The third ORF is a putative ORFAB transposase reconstructed in silico by a possible -1 frameshift.
ISPak1 has been identified by its integration to the entrapment vector pMAT1 (sacB cassette). As judged from DNA hybridization analysis ISPak1 is present in 1 copy in P. alkenifer DSM 11593 genome. Homologous sequences have been detected by DNA hybridization in P. aestuarii DSM 19484, P. alcaliphilus JCM 7364, P. aminophilus JCM 7686, P. aminovorans JCM 7685, P. halophilus JCM 14014, P. kondratievae NCIMB 13773T, P. koreensis JCM 21670, P. marcusii OS22, P. methylutens DM12, P. pantotrophus DSM 11072, P. pantotrophus DSM 11073, P. pantotrophus LMD 82.5, P. seriniphilus DSM 14827, P. solventivorans DSM 11592, P. sulfurooxidans JCM 14013, P. thiocyanatus JCM 20756 and P. versutus UW1.
At position 387, ISPak1 contains the sequence 5'-AAAAAAG-3' that might function as a -1 translational frameshifting site.
IRL of ISPak1 contains a sequence 5’-GACCCATTGAT-3’ matching (1 mismatch) to consensus sequence of integration host factor (IHF) binding site 5’-AANNNNTTGAT-3’.
References
1] Bartosik, D. (2010) Direct submission.

2] 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