ISMsi5

  • Family IS3
  • Group IS3
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
NC_011666 ND Methylocella silvestris
Methylocella silvestris BL2
DNA section
IS Length : 1228 bp

Ends


IR Length : 22/32

IRL : TGGACTTGCTCCGAAAAATGGGAAGCTCTTCTGAGGAAAAGAGGAGCATT
IRR : TGGACTTGCCGCGAGAAAGTGGAAAGCCTTTTCGACTCTACGCGGCCCGC

Insertion site


Left flankDirect repeatRight flankDR Length
CCGGTCACCCGATGGCGGCG0

DNA sequence

TGGACTTGCTCCGAAAAATGGGAAGCTCTTCTGAGGAAAAGAGGAGCATTTTATGGGCAAGCCGCAGCGCCGGTTCGGGAAGGAATTCGAGGCGGAAGCC
ATTCGTCTGGCCGAGACGAGCGGCCGAACGCAGCGTGAGATCGCCGAGGATCTCGGTATCGGGCTGTCGACCTTGCGCCGTTGGCTCGACAAGCGTCGGG
AGCATGATTTCGAAGCGCCGCCTCCCGAGCGGCAGGAGGATCTTGCGGCCGATTTGAAGCGTCTGCGGCGTGAGAACGAAATTCTGCGCCAGGAGCGCGG
GATCCTGAAGAGGGCCGCGACTTTTTTCGCCAAGGAGGGAAGTCGATGAGATTTGAGCTCATCGATGCGGCGAAGGAAGAGTTCCCCGTCCTGCGTATGT
GCAAGGTGCTCGGCGGCAGCGCCAGCGGGTATTTCGCCTGGAGGGAGCGCCCGGCCTGCCGCCGGCAGAAGGGCGACATGGTGTTGCTCGCCCATGTCCG
CTCGGCCTTCGCCTTATCGAATGAGACCTACGGCAGCCCCCGCATGCTGCGCGAACTGCGCGACAATGGTCTGTCGATCGGGCGTCGGCGCGTCGCCCGG
CTGATGCGAGAGAACGGGCTAGAGGCGCGGCAGAACGGCGCTTCAAGCGCACCACCGATAGCCTCCACGCCTTCCCGGTCGCTCCAAATCTCCTGGATCA
GGACTTCGCCGCGGCAGGCCGAACCAGAAGTGGGCGCCGATATCTCCTACGTTTGGACGCGGGCGGGATGGCTTTACCTTGCCGTCGTTATCGACCTCTT
CGCCCGGCGCATCGTCGGTTGGGCGACGAGCGACCGCCTCCATAAGGAACTGGCTTTGTCGGCGCTGCGTCGCGCCATTGCTTGGCGGCGACCCGGCGCC
GGGCTCATCCATCACGCGGATCGCGGCAGCACTGCGCTATCGACTACCAGGCTGAGCTGCGCCGCAGGGGCATCCTGATCTCGATGTCGGGCAAGGGAAA
CTGCTACGACAATGCGATGGTCGAAACCTTCTTCAAGACGCTGAAGACCGAACTCGTCTGGCGCACCGTCTTCCAGGACAGAGGCAACCGCCGCAATCGG
TCGTTATATCGACGGGTTCTACAACCCCGTCCGGCGACATTTGGCACTCGACTTCATCAACCCGCTCCAATTTGAGAGGCGGGCCGCGTAGAGTCGAAAA
GGCTTTCCACTTTCTCGCGGCAAGTCCA
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
297 bp98 aa53349+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MGKPQRRFGKEFEAEAIRLAETSGRTQREIAEDLGIGLSTLRRWLDKRREHDFEAPPPERQEDLAADLKRLRRENEILRQERGILKRAATFFAKEGSR

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
918 bp305 aa2741191+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

ERNSAPGARDPEEGRDFFRQGGKSMRFELIDAAKEEFPVLRMCKVLGGSASGYFAWRERPACRRQKGDMVLLAHVRSAFALSNETYGSPRMLRELRDNGL
SIGRRRVARLMRENGLEARQNGASSAPPIASTPSRSLQISWIRTSPRQAEPEVGADISYVWTRAGWLYLAVVIDLFARRIVGWATSDRLHKELALSALRR
AIAWRRPGAGLIHHADRGSTALSTTRLSCAAGAS*SRCRARETATTMRWSKPSSRR*RPNSSGAPSSRTEATAAIGRYIDGFYNPVRRHLALDFINPLQF
ERRAA

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
1139 bp379 aa531191+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MGKPQRRFGKEFEAEAIRLAETSGRTQREIAEDLGIGLSTLRRWLDKRREHDFEAPPPERQEDLAADLKRLRRENEILRQERGILKRAATFFRQGGKSMR
FELIDAAKEEFPVLRMCKVLGGSASGYFAWRERPACRRQKGDMVLLAHVRSAFALSNETYGSPRMLRELRDNGLSIGRRRVARLMRENGLEARQNGASSA
PPIASTPSRSLQISWIRTSPRQAEPEVGADISYVWTRAGWLYLAVVIDLFARRIVGWATSDRLHKELALSALRRAIAWRRPGAGLIHHADRGSTALSTTR
LSCAAGAS*SRCRARETATTMRWSKPSSRR*RPNSSGAPSSRTEATAAIGRYIDGFYNPVRRHLALDFINPLQFERRAA

 

Blast result :
Comments
ISMsi5 is 66% aa similar to ISNisp1. The third ORF is a putative ORFAB transposase reconstructed in silico by possible -1 frameshift.
The ORFB contains two STOP codons in frame.
References
1] ISfinder annotation (2009)
2] Lucas,S., Lucas,S., Lapidus,A., Glavina del Rio,T., Dalin,E., Tice,H., Bruce,D., Goodwin,L., Pitluck,S., Forester,B., Larimer,F., Land,M., Hauser,L., Kyrpides,N., Ovchinnikova,G., Dunfield,P.F., Dedysh,S.N., Liesack,W., Stott,M.B., Smirnova,A.V., Alam,M., Chen,Y., Murrell,J.C. and Richardson,P. (2008) Direct submission GenBank.