ISRel11

  • Family IS5
  • Group IS427
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
NC_004041 ND Rhizobium etli
Rhizobium etli CFN 42 symbiotic plasmid p42d
Rhizobium etli Kim 5
DNA section
IS Length : 862 bp

Ends


IR Length : 23/26

IRL : GGCTGTAGTGACAAATTAATGATTTGGGATTCCGTTTTGGGAGCAAATCA
IRR : GGCTGCAGTGACAATTTAATCATTTGAGCCAGAGCATGATGGCGGCGATT

Insertion site


Left flankDirect repeatRight flankDR Length
CCTGCTAGACTAGAACGTGGTG2
CTCGAGGAACTAGCAGTTTCCT2

DNA sequence

GGCTGTAGTGACAAATTAATGATTTGGGATTCCGTTTTGGGAGCAAATCAGATTCAACGCTGACTTTTGGAGGTTGGCGATGGATGGTGAGGTTCTTCGA
GACGATCAATGGGAGCGGCTGACGCCGTTAGTGCCCGGCGGTCGCAAAGGCCGGCGCGGTCCGCGTAGTGACGGACGCCGGTTCTTCGATGCGGTGTTGT
GGCTCGCCCGGTCGGGTGCGCGCTGGCGTGATCTGCCGGAAGACCGCTTCGGCCCCTATCAGACGATCAAACGGCGCTACTATCGCTGGATCGAACAGGG
CATCTTCGACAAGATTTTCGAAGCCGTCGCGATCGATCCGGATATGGAGTGGTTGTCCATCGACGCCACGGTGATCCGGGCACAAGCGCAAGCGGCAGGC
GGACGCCGAAAAAGGGGGGACCGCAAGCCCAGGCTCTCGGCCGTTCCCGCGGGGGATTTGGCAGCAAGATCCATGCAGTAGTCGATGCGCTCGGCTTGCC
GGTGCGCCTTCACCTGGGACCCGGCCAGCAGAATGATATGGCGCCTGCCTGCGATCTCGTCCGGGGGCTGCCGGCCAAGCAGGTGCTCGCCGACCGCGCC
TATGACGCCGACAGCCTGCATGACATTATTCTCGAACAAGGTGGCGAACCGGTCATTCCACCACGCCGTCATCGAAAGTATCAGCATGCCTACGACCGTA
TCGCCTACAAGGCCCGCTGGGGGATCGAGAGCTTCTTTGCAAAGCTCAAGCAATGGCGGCGAATCGCAACGCGCTACGACAAAGTCGCCGCCAACTTCAT
GGGATTCATCAAAATCGCCGCCATCATGCTCTGGCTCAAATGATTAAATTGTCACTGCAGCC
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
402 bp133 aa80481+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MDGEVLRDDQWERLTPLVPGGRKGRRGPRSDGRRFFDAVLWLARSGARWRDLPEDRFGPYQTIKRRYYRWIEQGIFDKIFEAVAIDPDMEWLSIDATVIR
AQAQAAGGRRKRGDRKPRLSAVPAGDLAARSMQ

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
612 bp203 aa232843+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

SAGRPLRPLSDDQTALLSLDRTGHLRQDFRSRRDRSGYGVVVHRRHGDPGTSASGRRTPKKGGPQAQALGRSRGGFGSKIHAVVDALGLPVRLHLGPGQQ
NDMAPACDLVRGLPAKQVLADRAYDADSLHDIILEQGGEPVIPPRRHRKYQHAYDRIAYKARWGIESFFAKLKQWRRIATRYDKVAANFMGFIKIAAIML
WLK

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
764 bp254 aa80843+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MDGEVLRDDQWERLTPLVPGGRKGRRGPRSDGRRFFDAVLWLARSGARWRDLPEDRFGPYQTIKRRYYRWIEQGIFDKIFEAVAIDPDMEWLSIDATVIR
AQAQAAGGRRKKGGPQAQALGRSRGGFGSKIHAVVDALGLPVRLHLGPGQQNDMAPACDLVRGLPAKQVLADRAYDADSLHDIILEQGGEPVIPPRRHRK
YQHAYDRIAYKARWGIESFFAKLKQWRRIATRYDKVAANFMGFIKIAAIMLWLK

 

Blast result :
Comments
ISRel11 is 86% aa similar to ISCc1.
The third ORF is a putative ORFAB transposase reconstructed in silico by a possible -1 frameshift.
References
1] Lozano LF (2010) Direct submission.
2] González V, Santamaría RI, Bustos P, Hernández-González I, Medrano-Soto A, Moreno-Hagelsieb G, Janga SC, Ramírez MA, Jiménez-Jacinto V, Collado-Vides J, Dávila G. (2006) PNAS. 7;103(10):3834-9
3] Gonzalez V, Bustos P, Ramirez-Romero M.A, Medrano-Soto A, Salgado H, Hernandez-Gonzalez I, Hernandez-Celis JC, Quintero V, Moreno-Hagelsieb G, Girard L, Rodriguez O, Flores M, Cevallos MA, Collado-Vides J, Romero D, and Davila G. (2003) Genome Biol. 4 (6), R36
4] Quintero V, Cevallos MA, and Davila G. (2002) Mol. Microbiol. 46 (4), 1023-1032
5] Ramirez-Romero MA, Bustos P, Girard L, Rodriguez O, Cevallos MA, and Davila G. (1997) Microbiology (Reading, Engl.) 143 (PT 8), 2825-2831
6] Girard ML, Flores M, Brom S, Romero D, Palacios R, and Davila G. (1991) J. Bacteriol. 173 (8), 2411-2419