ISMac16

  • Family IS1
  • Group
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
NC_003552 ND Methanosarcina acetivorans
Methanosarcina acetivorans C2A
DNA section
IS Length : 740 bp

Ends


IR Length : 20/24

IRL : GGTATTGGTAGTTAATTATAGTTATATATTATGAAAACCTATATTTCTGC
IRR : GGTATTGTTAATTAAATATAGATAACTCTTTATTTCTGTTTTTCATCAAT

Insertion site


Left flankDirect repeatRight flankDR Length
GAAGATAAAGAAAATAAAAAGAATAAAAG8
AGAAAAAATTAGTACGAAATGTTTATCGATAT8
AAAGCGCACTTAAATTTGCAGTTAGTTCAGAA8

DNA sequence

GGTATTGGTAGTTAATTATAGTTATATATTATGAAAACCTATATTTCTGCATGAACTGCCCAAGATGCAAAAGTTCCAATCACACAAAAAACGGTATAGT
TTGTGGACGTCAACGCTACAAATGCCACGATTGTGGATATAACTATTCAGTCGAGCTAAAATCAACTGCTAGTTCTCCTTTAGTTAAGAGACAGGCTTTG
CAACTTTATCTTGAAGGATTAGGATTTCGCTCAATAGGACGATTTTTAGGGGTAAGTCATGTTTCTGTCCAAAAATGGATAAAGAAATTTGGTCAGGAGA
TAGAGGAGCTAAAAAGCGAAAATGAGATATCTATTGTTGAACTGGATGAGATGCACACTTACATCAGTAACAAAAAAAATATTGCTGGATCTGGATTGCT
GTTGATAGAGTTGGGAAAAAGTTCATCAACTGCTCTTTTGGTAGCAGAGGAACGAAAACTGGACAACTACTCTGGGAAAAATTAAAGAAGAAAGAGATTG
GAGAGGTGATGACTGATCACTGGAGGGCATATGCAGAGTTTATTCCTGAAAATATTCATACTCAATCCAAAGCAGAAACGTATACAGTTGAAGGATATAA
CGGCATACTAAGGCACTTTCTGGCAAGGTTGAGACGAAAGACAAAGTGTTATACGAAGAGTCTTGAAATGCTAAAGTACTCTGCTCTTCTATTGATGAAA
AACAGAAATAAAGAGTTATCTATATTTAATTAACAATACC
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
435 bp144 aa51485+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MNCPRCKSSNHTKNGIVCGRQRYKCHDCGYNYSVELKSTASSPLVKRQALQLYLEGLGFRSIGRFLGVSHVSVQKWIKKFGQEIEELKSENEISIVELDE
MHTYISNKKNIAGSGLLLIELGKSSSTALLVAEERKLDNYSGKN

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
363 bp120 aa371733+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

QKKYCWIWIAVDRVGKKFINCSFGSRGTKTGQLLWEKLKKKEIGEVMTDHWRAYAEFIPENIHTQSKAETYTVEGYNGILRHFLARLRRKTKCYTKSLEM
LKYSALLLMKNRNKELSIFN

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
683 bp226 aa51733+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MNCPRCKSSNHTKNGIVCGRQRYKCHDCGYNYSVELKSTASSPLVKRQALQLYLEGLGFRSIGRFLGVSHVSVQKWIKKFGQEIEELKSENEISIVELDE
MHTYISNKKYCWIWIAVDRVGKKFINCSFGSRGTKTGQLLWEKLKKKEIGEVMTDHWRAYAEFIPENIHTQSKAETYTVEGYNGILRHFLARLRRKTKCY
TKSLEMLKYSALLLMKNRNKELSIFN

 

Blast result :
Comments
ISMac16 is 57% (ORFA) and 54% (ORFB) aa similar to ISMae3.
There are 16 complete copies and 7 partial copies in Methanosarcina acetivorans C2A genome.
There are a -1 frameshift site at position 374 : AAAAAAT. The third ORF is the ORF AB, fusion in silico.
References
1] Galagan,J.E., Nusbaum,C., Roy,A., Endrizzi,M.G., Macdonald,P., FitzHugh,W., Calvo,S., Engels,R., Smirnov,S., Atnoor,D., Brown,A., Allen,N., Naylor,J., Stange-Thomann,N., DeArellano,K., Johnson,R.,
Linton,L., McEwan,P., McKernan,K., Talamas,J., Tirrell,A., Ye,W.,Zimmer,A., Barber,R.D., Cann,I., Graham,D.E., Grahame,D.A., Guss,A.M., Hedderich,R., Ingram-Smith,C., Kuettner,H.C., Krzycki,J.A., Leigh,J.A., Li,W., Liu,J., Mukhopadhyay,B., Reeve,J.N., Smith,K., Springer,T.A., Umayam,L.A., White,O., White,R.H., Conway de Macario,E., Ferry,J.G., Jarrell,K.F., Jing,H., Macario,A.J., Paulsen,I., Pritchett,M., Sowers,K.R., Swanson,R.V., Zinder,S.H., Lander,E., Metcalf,W.W. and Birren,B. (2002) Genome Res. 12 (4), 532-542