ISMra4

  • Family IS3
  • Group IS3
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
NC_010510 ND Methylobacterium radiotolerans
Methylobacterium radiotolerans JCM 2831 plasmid pMRAD01
DNA section
IS Length : 1237 bp

Ends


IR Length : 20/27

IRL : TGGACTTGTCTCGAGAAAGTGGAGAGCTCTTTTCCTGAAGGAGGAGGGTT
IRR : TGGACTTGCTTCAGTTCAGTGGAGAGCAGCTTGGTGGTTGATACCCCTCT

Insertion site


Left flankDirect repeatRight flankDR Length
CGGTTTGCGGTCGAGCGCCT0

DNA sequence

TGGACTTGTCTCGAGAAAGTGGAGAGCTCTTTTCCTGAAGGAGGAGGGTTCCGATGGCAGACCGGAAGCAGACCTTTACCCCTGAGTTTCGTGCTGAGGC
GGTGCGATTGGCGCAGACAAGTGGGCGGTCGCGCCGCGAGGTCGCCGCCGATCTCGGCGTCGGGCTCTCGACGCTGCGCAACTGGATCGACGGTCGACGT
GAGCGAGAGATGGACAACCCACCGGCCGACCGGCAGGAGGACATGGCCGCCGAGCTCAAGCGTCTGCGCCGCGAGAACGAGGTGCTGCGCCAGGAGCGGG
AGATCCTGAGGCGGGCCACGGCTTTTTTCGCCAAGGAGGGAAGTCGATGAGGTTCCGCCTCATCGACGCGGCGAAGAAGGACTTCCCGGTCGCGCGCCTG
TGCAAGGTCCTCGACGTCAGTCCGAGCGGCTATTTCGCCTGGAAGAACCGCCCGGCCTCGACGCGGCAGCGCGAGGATCTCGTGCTGCTTGCCCACGTCC
GATCCGCCTTCACGCTCTCGCACGAGACGTATGGCAGCCCGCGCATGACCCACGAGTTGCGCGAGCAGGGCCTGGCGGCAGGCCGGCGGCGCGTGGCCCG
GCTGATGCGGGAGAACGGGCTCAAAGCCCGCCAGCCGCGCCGCTTCCGGCGCACGACGGACAGCGGCCACGCCTTTCCGGTCGCGCCCAACCACCTCGAC
CAGGACTTCACGGCGGCCGGGCCGGACCGCAAGTGGGGAAGCGACATCTCCTACATCTGGACGCGGGAGGGCTGGTTGTACCTGGCGGTGGTCCTCGATC
TGTACTCCCGACGGGTCGTGGGCCGGGCGGCGGGCGACCGGCTTCACAAGGAGCTCGCGCTGACCGCGCTGCGACGTGCCCTTGTCGTCCGACGGCCCGG
ACCAGGTTTATTTCATCATTCCGACCGCGGCAGTCAGTACTGTTCGAATGAGTATCAGGCGGAACTACGAGGACATGGCATCGTGATCTCGATGTCCGGC
AAGGGAAATTGTTATGACAACGCGATGGTCGAGACGTTCTTCAAGACGCTGAAGAGCGAGTTGGTCTGGCGCACCGCGTTCCAGACGCGAGCCGAGGCCA
CCATCGCGCTGGCCCGTTACATCGATGGCTTTTACAATCCCTGCCGCCGTCACTCGGCGCTGGGCTTCACAAGCCCCACCCAGTTCGAGAGGGGTATCAA
CCACCAAGCTGCTCTCCACTGAACTGAAGCAAGTCCA
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 aa54350+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MADRKQTFTPEFRAEAVRLAQTSGRSRREVAADLGVGLSTLRNWIDGRREREMDNPPADRQEDMAAELKRLRRENEVLRQEREILRRATAFFAKEGSR

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
1020 bp339 aa2031222+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

ARDGQPTGRPAGGHGRRAQASAPRERGAAPGAGDPEAGHGFFRQGGKSMRFRLIDAAKKDFPVARLCKVLDVSPSGYFAWKNRPASTRQREDLVLLAHVR
SAFTLSHETYGSPRMTHELREQGLAAGRRRVARLMRENGLKARQPRRFRRTTDSGHAFPVAPNHLDQDFTAAGPDRKWGSDISYIWTREGWLYLAVVLDL
YSRRVVGRAAGDRLHKELALTALRRALVVRRPGPGLFHHSDRGSQYCSNEYQAELRGHGIVISMSGKGNCYDNAMVETFFKTLKSELVWRTAFQTRAEAT
IALARYIDGFYNPCRRHSALGFTSPTQFERGINHQAALH

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
1169 bp389 aa541222+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MADRKQTFTPEFRAEAVRLAQTSGRSRREVAADLGVGLSTLRNWIDGRREREMDNPPADRQEDMAAELKRLRRENEVLRQEREILRRATAFFRQGGKSMR
FRLIDAAKKDFPVARLCKVLDVSPSGYFAWKNRPASTRQREDLVLLAHVRSAFTLSHETYGSPRMTHELREQGLAAGRRRVARLMRENGLKARQPRRFRR
TTDSGHAFPVAPNHLDQDFTAAGPDRKWGSDISYIWTREGWLYLAVVLDLYSRRVVGRAAGDRLHKELALTALRRALVVRRPGPGLFHHSDRGSQYCSNE
YQAELRGHGIVISMSGKGNCYDNAMVETFFKTLKSELVWRTAFQTRAEATIALARYIDGFYNPCRRHSALGFTSPTQFERGINHQAALH

 

Blast result :
Comments
ISMra4 is 78% aa similar to ISNisp1.
The third ORF is a putative ORFAB transposase reconstructed in silico by a possible -1 frameshift.
References
1] Ming-Chun Lee and David Robinson (2009) Direct submission.
2] Copeland,A., Lucas,S., Lapidus,A., Glavina del Rio,T., Dalin,E., Tice,H., Bruce,D., Goodwin,L., Pitluck,S., Kiss,H., Brettin,T., Detter,J.C., Han,C., Kuske,C.R., Schmutz,J., Larimer,F., Land,M., Hauser,L., Kyrpides,N., Mikhailova,N., Marx,C.J. and Richardson,P. (2008) Direct submission Genbank.