ISRpa2

  • Family IS3
  • Group IS407
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
NC_005296 ND Rhodopseudomonas palustris
Rhodopseudomonas palustris CGA009
DNA section
IS Length : 1265 bp

Ends


IR Length : 36/46

IRL : TGACCTTGCCCCTCGGGCTTAATCCAGTTTGAAGTTCGTTCTGGCCCTAA
IRR : TGACCTTGCCCCCAAGTTTTATCCAGGTCTGAGTTCGTTCGGGTGGTTAG

Insertion site


Left flankDirect repeatRight flankDR Length
GACTTCACCTCGTCGGCCGGGTTT4

DNA sequence

TGACCTTGCCCCTCGGGCTTAATCCAGTTTGAAGTTCGTTCTGGCCCTAACGAGGACCAGAGCATGAAGCGCAGCCGCTTTTCGGAAGAGCAGATCATCG
GGATTTTGAAGGAGCACGAGGCTGGTGTTTCGGTCGCCGATCTTTGCCGCAAGCACGGCGTCAGCGACGCCAGCATCTATAAGTGGAAGGCGAAGTTTGG
CGGGATGGACGTCTCGGAGGCCAAGCGATTGAAGTCGCTGGAGGACGAGAACACCCGGCTGAAGCGGTTGCTGGCCGACGCCATGCTGGACAATGCAGCC
CTGAAGGATCTTCTGGGAAAGAAGTGGTGACGCCCGCGGCCAAGCGGAAAGCTGTCGCGCATCTGCAAACTGCATTCGAGATGAGCGAACGGCGGGCGTG
TAAAGCCATCGGCTGCTGCCGCATGACAGTCAGATATCAGACGAGCCGGAGCGATGATGCCGGGCTGCGCCAACGTATGAGGGCGATCGCCCATGAGCGC
CGGCGCTTTGGCTATCGGCGCCTCCACGTCCTGCTCAAGCGTGAGGGCTACCTGGTCAATCACAAGAAGCTGTTCCGGCTGTACCGTGAGGAGAAGCTCA
CAGTGCGCCGCAGGGGTGGCCGCAAACGGGCCCTCGGCACACGAGCTCCCATGACAGTGCCGGTGCTCCCGAATGATCGCTGGTCGCTCGACTTCGTGTC
GGATCAGATGACCGATGGTCGACGCTTCCGCATTCTGACTGTGGTCGACGACTGCACCCGCGAGTGCCTGGCGCTGGTGGTCGACACCTCGCTCTCGGGC
GCCCGGGTCGCACGAGAACTGGACCGGCTGGTTGCCGAGCGCGGCAAGCCCAAGATGGTGGTGAGCGACAATGGCAGCGAGTTCACCAGCAATGCCATCC
TGACATGGGCCGATCAGAGCCGTATCGCCTGGCACTACATTGCGCCGGGAAAACCCATGCAAAACGCCTTCATCGAGAGCTTCAACGGCCGCCTGCGGGA
TGAACTGCTGAACGAAACGCTGTTCACCTCGCTGGCCCAGGCCCGCGTAGCGCTCCGGTGCTGGCGGGCCGACTACAATGATGCACGACCGCACTCACAG
CTCGGGTGGCGGACGCCATCCGAGTTCGCCGCCACCTGCAATCCGCGTCGGGATCTGGCGCTGCGCTATATCGAAAGCTCCACGCCAGCTCCCGCCACCG
CCCACATGGGCCCATCTAACCACCCGAACGAACTCAGACCTGGATAAAACTTGGGGGCAAGGTCA
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
267 bp88 aa64330+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MKRSRFSEEQIIGILKEHEAGVSVADLCRKHGVSDASIYKWKAKFGGMDVSEAKRLKSLEDENTRLKRLLADAMLDNAALKDLLGKKW

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
1065 bp354 aa1831247+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

VEGEVWRDGRLGGQAIEVAGGREHPAEAVAGRRHAGQCSPEGSSGKEVVTPAAKRKAVAHLQTAFEMSERRACKAIGCCRMTVRYQTSRSDDAGLRQRMR
AIAHERRRFGYRRLHVLLKREGYLVNHKKLFRLYREEKLTVRRRGGRKRALGTRAPMTVPVLPNDRWSLDFVSDQMTDGRRFRILTVVDDCTRECLALVV
DTSLSGARVARELDRLVAERGKPKMVVSDNGSEFTSNAILTWADQSRIAWHYIAPGKPMQNAFIESFNGRLRDELLNETLFTSLAQARVALRCWRADYND
ARPHSQLGWRTPSEFAATCNPRRDLALRYIESSTPAPATAHMGPSNHPNELRPG

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
1184 bp394 aa641247+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MKRSRFSEEQIIGILKEHEAGVSVADLCRKHGVSDASIYKWKAKFGGMDVSEAKRLKSLEDENTRLKRLLADAMLDNAALKDLLGKEVVTPAAKRKAVAH
LQTAFEMSERRACKAIGCCRMTVRYQTSRSDDAGLRQRMRAIAHERRRFGYRRLHVLLKREGYLVNHKKLFRLYREEKLTVRRRGGRKRALGTRAPMTVP
VLPNDRWSLDFVSDQMTDGRRFRILTVVDDCTRECLALVVDTSLSGARVARELDRLVAERGKPKMVVSDNGSEFTSNAILTWADQSRIAWHYIAPGKPMQ
NAFIESFNGRLRDELLNETLFTSLAQARVALRCWRADYNDARPHSQLGWRTPSEFAATCNPRRDLALRYIESSTPAPATAHMGPSNHPNELRPG

 

Blast result :
Comments
ISRpa2 is 93 % (ORFA) aa similar to ISR1 and 82% (ORFB) aa similar to ISRle4. The third ORF is a putative ORFAB transposase reconstructed in silico by possible -1 frameshift.
References
1] Larimer,F.W., Chain,P., Hauser,L., Lamerdin,J., Malfatti,S., Do,L., Land,M.L., Pelletier,D.A., Beatty,J.T., Lang,A.S., Tabita,F.R., Gibson,J.L., Hanson,T.E., Bobst,C., Torres,J.L., Peres,C., Harrison,F.H., Gibson,J. and Harwood,C.S. Nat. (2004) Biotechnol. 22 (1), 55-61