ISPye11

  • Family IS5
  • Group IS427
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
CP020442 ND Paracoccus yeei
Paracoccus yeei
Paracoccus yeei FDAARGOS_252
Paracoccus yeei CCUG 46822
DNA section
IS Length : 840 bp

Ends


IR Length : 12/16

IRL : GAGTCAGGACCTATAAATTTCCTTGAGCGCCGGCGGGCGGCATGATTCAA
IRR : GAGTCAGGGCTCACAACCCATAGATGACGGTTGCGGCGAGAGCGCAGGCT

Comments : Empty insertion sites in other Paracoccus yeei strains enabled precisely defining ends and DRs.

Insertion site


Left flankDirect repeatRight flankDR Length
cgcacgctgcTAgggctgaccc2
actgaactgtTAgcattacggt2

DNA sequence

GAGTCAGGACCTATAAATTTCCTTGAGCGCCGGCGGGCGGCATGATTCAAACTCCCGACTTGGGGAGGGATCATGAGCGCGCTTTATTGGCTGACAGATG
CGCAGATAGAGCGGCTGCGGCCGTTCTTTCCGAAGTTCCGAGGCAGGCCGAGGGTCGATGACCGGCGCGTTCTGAGCGGGATAATCTTGATCCAGCGCAA
TGGGTTGATGTGGAAGCATGCTCCGGCCGCCTATGGCCCGCCGAAGACGCTTTGCAGCCGCTGGAAGCGGTGGATCCGGATGGGCGTGTTCGCCACGATC
ATGACCGAACTGGCCGTCCAGGCCCAGGAAACCCGGATCGTCATGATCGACGCGACCCATGCGAAGGCGCATCGAACCGCATCGAGCCTGGCGGTTCAAA
AAGGGGGCGCGGACGGCTGATCGGGCGCACGAAGGGCGGTCTGAACTCGAAACTGCACGTCCTGGCGGATGCGAAGGGCCGTCCGATCCAGATGTTCCTG
TCAGCGGGGCAGACCTCCGACTGCATCGGCGCGCGGGCGCTGCTGTCCTCGATCCCCTCGGCCGGGGCGTTGCTTGCAGACCGGGGCCATGACGCCGACT
GGTTCCGCAACGCGCTGATCGAGAGGGGCATTTCGCCGTGCATCCCCTCCCGCACCGGCCGCAAGGCCCCGATCCCGCACGACGCCAGCATCTATCGCCT
GCGTCACCGGATCGAGAACATGTTCGCACGCCTCAAGGATTGGCGGCGGATCGCAATCCGATACGACCGCTGCCCGATCCTGTTCCTCTCAGCCTGCGCT
CTCGCCGCAACCGTCATCTATGGGTTGTGAGCCCTGACTC
Recoding section
  • Recoding by frameshift
  • Frame -1
  • Type transcriptional
  • Experimentally demonstrated No

Stimulators :

  • Shine-Dalgarno sequence :
  • Secondary structure :

Recoding motif :

Protein section
ORF number : 3

 

ORF 1
LengthBeginEndStrandFusion ORF
345 bp115 aa73417+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MSALYWLTDAQIERLRPFFPKFRGRPRVDDRRVLSGIILIQRNGLMWKHAPAAYGPPKTLCSRWKRWIRMGVFATIMTELAVQAQETRIVMIDATHAKAH
RTASSLAVQKGGADG

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
666 bp222 aa162827+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

PARSERDNLDPAQWVDVEACSGRLWPAEDALQPLEAVDPDGRVRHDHDRTGRPGPGNPDRHDRRDPCEGASNRIEPGGSKRGRGRLIGRTKGGLNSKLHV
LADAKGRPIQMFLSAGQTSDCIGARALLSSIPSAGALLADRGHDADWFRNALIERGISPCIPSRTGRKAPIPHDASIYRLRHRIENMFARLKDWRRIAIR
YDRCPILFLSACALAATVIYGL

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
755 bp252 aa73827+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MSALYWLTDAQIERLRPFFPKFRGRPRVDDRRVLSGIILIQRNGLMWKHAPAAYGPPKTLCSRWKRWIRMGVFATIMTELAVQAQETRIVMIDATHAKAH
RTASSLAVQKGGRGRLIGRTKGGLNSKLHVLADAKGRPIQMFLSAGQTSDCIGARALLSSIPSAGALLADRGHDADWFRNALIERGISPCIPSRTGRKAP
IPHDASIYRLRHRIENMFARLKDWRRIAIRYDRCPILFLSACALAATVIYGL

 

Blast result :
Comments
ISPye11 is 77% aa similar to ISPam4.
ISPye11 was identified by in silico sequence analysis of Paracoccus yeei strains: CCUG 46822 (9 copies of ISPye11 and isoforms of ISPye11) and FDAARGOS_252 (1 isforoms).
The third ORF is the putative ORFAB transposase reconstructed in silico by possible -1 frameshift.
References
1] Chmielowska C., Szuplewska M., Bartosik D. (2018) Direct submission.
2] Goldberg,B., Campos,J., Tallon,L., Sadzewicz,L., Sengamalay,N., Ott,S., Godinez,A., Nagaraj,S., Vavikolanu,K., Aluvathingal,J., Nadendla,S. and Sichtig,H. (2017) Direct GenBank submission.