ISPam4

  • Family IS5
  • Group IS427
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
NC_010847 ND Paracoccus aminophilus
Paracoccus aminophilus plasmid pAMI2
DNA section
IS Length : 865 bp

Ends


IR Length : 13/15

IRL : GGTTCAGGACCCATTGATTTGCTTGAGGCTGGGCGGGTTGCGTGATTCAA
IRR : GGGTCAGGACTCATTCTTGTTTCATAGCCAGAAGATGACGGTTGCAGCGA

Insertion site


Left flankDirect repeatRight flankDR Length
CTGTCGGGCCTATTTTGATGCT2

DNA sequence

GGTTCAGGACCCATTGATTTGCTTGAGGCTGGGCGGGTTGCGTGATTCAAGCTCCCGAACTGACGGGGGTGATGATGAGCAACCTTTACTGGCTGACGGA
CGACCAGATGGAGCGGCTGCGGCCCTTCTTTCCGAAGAGCCATGGTCGTCCACGGGTCGATGACCGGCGCGTTCTGAGTGGGATAATTTTCATCAACCGC
AATGGGTTGCGTTGGTGTGATGCTCCGCCCGAGTACGGTCCGCCGAAGACGCTCTACAACCGCTGGGTCCGCTGGAGCCGGATGGGGGTTTTCGCCCGGA
TGATGGTGGGGCTGGCCTCCGGGGGTGGTGAGGAGAAGGTCGTGATGATCGACGCGACGTATCTCAAGGCGCACCGTACGGCTTCGAGCCTGCGGGTCAA
AAAGGGGGGGCCGACGACAAGCGCGGGCGTCTGATCGGTCGCACGAAGGGCGGACTGAACACCAAGTTGCACGCGGTCACGGATGCCATAGGCCGCCCGA
TCCGCTTCTTCATGACGGCGGGCCAGGTCAGCGACTACATCGGTGCGGCGGCCTTGCTGGACTGCCTGCCGGATGCAGATTGGCTGATCGCCGACCGTGG
CTATGACGCCGACTGGCTCCGGGATGCCTTGAAAGACAAGGGGATAAAGCCCTGCATCCCCGGCCGGAAGTCGCGCGGCAAGCCCATCAAGCACGACAAG
CGCCGCTACAAACGGCGCAACCGGATCGAGATCATGTTCGGCAGGCTCAAGGACTGGCGCCGCGTTGCCACCCGCTACGACAGGTGCCCAAAGGTCTTCC
TCGCCGCCGTCACACTCGCTGCAACCGTCATCTTCTGGCTATGAAACAAGAATGAGTCCTGACCC
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
360 bp119 aa75434+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MSNLYWLTDDQMERLRPFFPKSHGRPRVDDRRVLSGIIFINRNGLRWCDAPPEYGPPKTLYNRWVRWSRMGVFARMMVGLASGGGEEKVVMIDATYLKAH
RTASSLRVKKGGPTTSAGV

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
513 bp170 aa332844+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

GEGRDDRRDVSQGAPYGFEPAGQKGGADDKRGRLIGRTKGGLNTKLHAVTDAIGRPIRFFMTAGQVSDYIGAAALLDCLPDADWLIADRGYDADWLRDAL
KDKGIKPCIPGRKSRGKPIKHDKRRYKRRNRIEIMFGRLKDWRRVATRYDRCPKVFLAAVTLAATVIFWL

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
770 bp256 aa75844+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MSNLYWLTDDQMERLRPFFPKSHGRPRVDDRRVLSGIIFINRNGLRWCDAPPEYGPPKTLYNRWVRWSRMGVFARMMVGLASGGGEEKVVMIDATYLKAH
RTASSLRVKKGGADDKRGRLIGRTKGGLNTKLHAVTDAIGRPIRFFMTAGQVSDYIGAAALLDCLPDADWLIADRGYDADWLRDALKDKGIKPCIPGRKS
RGKPIKHDKRRYKRRNRIEIMFGRLKDWRRVATRYDRCPKVFLAAVTLAATVIFWL

 

Blast result :
Comments
The third ORF is a putative ORFAB transposase reconstructed in silico by a possible -1 frameshift.
ISPam4 (orfAB) is 87% aa similar to ISRhsp4.
ISPam4 has been identified in silico form the nucleotide sequence of plasmid pAMI2. At position 399, ISPam4 carries a sequence 5'-AAAAAG-3' that might function as a -1 translational frameshifting site. IRL of ISPam4 contains a sequence 5’-GACCCATTGAT -3’ matching (1 mismatch) to consensus sequence of integration host factor (IHF) binding site 5’-AANNNNTTGAT-3’.
References
1] Dziewit,L., Jazurek,M., Drewniak,L., Baj,J. and Bartosik,D. (2007) J. Bacteriol. 189 (5), 1983-1997
2] Dziewit, L., Dmowski, M., Baj, J., and Bartosik, D. (2010) Appl. Environ. Microbiol. 76, 1861-1869.
3] 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