ISMex42

  • Family IS5
  • Group IS427
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
NC_010172 ND Methylobacterium extorquens
Methylobacterium extorquens PA1
DNA section
IS Length : 841 bp

Ends


IR Length : 18/23

IRL : GGCCTGTTGTCGCTTGAACGGATTGCCAACTCTGGCGTTTTCTCGTTTTC
IRR : GTCCTGTTGTCACTTGATCCAATCGAGCGTTGCGGCAAGGCAGAGAACGC

Insertion site


Left flankDirect repeatRight flankDR Length
GCAACCCGCTTGACTAGCAAGACAGTCGCT4

DNA sequence

GGCCTGTTGTCGCTTGAACGGATTGCCAACTCTGGCGTTTTCTCGTTTTCAAGTGAGGAGGCGTGATGCTGTCGGACGCGCAGTGGGATGAGTTGGAGCC
GTTGATCGAGGCCTGTCGCCCAAAGGCCAAGACGCCGCCTCAGGAGCTTCGGCGCACGATCTCGGCCATCCTCTGGCGGCATCAGAACGGGGCCAAGTGG
CGGGCCATCCCCGAGGAATTGGGCCCTTGGTGGCGCGCTGCTCAGATCTTCATCCGGTGGGCGCGCGCCGGGGTGTGGGAGCGGTTGCTCGACCGCGTGC
AGGAGCGCGGTCTCGCACTGGGCATGGTCTTCCTCGACGGCAGCAACGTGCGGGCTCATCAGAAGGCGGCGGGCGCTGCAAAAAGGGGGGATCTGCGGCC
GAGCGAGACCATCGTGAAGCGCTTGGCCGCTCAGGTGGCGGCTATGGCACCAAAGCCTGCGTGATCGCCGACGGAGCGGGCCGCGCCGTCGCCTTCCGCA
TCGCCCCGGGGCAGGCGCACGAACTGCCCCATGCCATCCCGTTGCTCGACCAATTGCCCGGTGTGCCGAAGTGGGTGGTGGGCGACCGCGGCTACTCCAG
CCACGGCTTCCGCGACCACATCTGGAAGGCAGGCGCCCGGCCCGCGATCCCGACCAAACGCAACGAGGCCCCGGTCGCCTGCCCGAGTTGGGTCTACAAC
AACCGCAACATCGTCGAGCGGCTCTGGGCGCGCCTCAAGAAGTGGCGGGCCGTGGCAACCCGATACGAGAAGACCGCCCTCAGCTTCACCGGCGTTCTCT
GCCTTGCCGCAACGCTCGATTGGATCAAGTGACAACAGGAC
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
399 bp132 aa66464+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MLSDAQWDELEPLIEACRPKAKTPPQELRRTISAILWRHQNGAKWRAIPEELGPWWRAAQIFIRWARAGVWERLLDRVQERGLALGMVFLDGSNVRAHQK
AAGAAKRGDLRPSETIVKRLAAQVAAMAPKPA

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
741 bp246 aa92832+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

VGAVDRGLSPKGQDAASGASAHDLGHPLAASERGQVAGHPRGIGPLVARCSDLHPVGARRGVGAVARPRAGARSRTGHGLPRRQQRAGSSEGGGRCKKGG
SAAERDHREALGRSGGGYGTKACVIADGAGRAVAFRIAPGQAHELPHAIPLLDQLPGVPKWVVGDRGYSSHGFRDHIWKAGARPAIPTKRNEAPVACPSW
VYNNRNIVERLWARLKKWRAVATRYEKTALSFTGVLCLAATLDWIK

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
767 bp255 aa66832+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MLSDAQWDELEPLIEACRPKAKTPPQELRRTISAILWRHQNGAKWRAIPEELGPWWRAAQIFIRWARAGVWERLLDRVQERGLALGMVFLDGSNVRAHQK
AAGAAKKGGSAAERDHREALGRSGGGYGTKACVIADGAGRAVAFRIAPGQAHELPHAIPLLDQLPGVPKWVVGDRGYSSHGFRDHIWKAGARPAIPTKRN
EAPVACPSWVYNNRNIVERLWARLKKWRAVATRYEKTALSFTGVLCLAATLDWIK

 

Blast result :
Comments
ISMex42 is 53% aa similar to ISCc1.
The third ORf is a putative ORFAB transposase reconstructed in silico by possible -1 frameshift.
References
1] Stephane Vuilleumier et.al. Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources. (2009) PLoS ONE Submitted.
2] Copeland,A., Lucas,S., Lapidus,A., Barry,K., Glavina del Rio,T., Dalin,E., Tice,H., Pitluck,S., Saunders,E., Brettin,T., Bruce,D., Detter,J.C., Han,C., Schmutz,J., Larimer,F., Land,M., Hauser,L., Kyrpides,N., Kim,E., Marx,C. and Richardson,P. (2007) Direct submission GenBank.