IS1R

  • Family IS1
  • Group
MGE type ISRelated element(s) :
Isoform IS1ASynonym(s)
Accession numberTranspositionOriginHost
J01730 ND Escherichia coli
Shigella flexneri 2a
Escherichia coli plasmid pR100
Acinetobacter baumannii SAK
DNA section
IS Length : 768 bp

Ends


IR Length : 18/23

IRL : GGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTG
IRR : GGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGTTAATGCCCGA

Insertion site


Left flankDirect repeatRight flankDR Length

DNA sequence

GGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGAC
GGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTATCTCTGCTCTCACTGCCGTAAAACATGGCAACTGCAGTTCACTTACACCGCTTCTC
AACCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTTGGATGCCGGGCAACCGCCCGCATTATGGGCGTTGGCCTCAACACGATTTTCCG
CCATTTAAAAAACTCAGGCCGCAGTCGGTAACCTCGCGCATACAGCCGGGCAGTGACGTCATCGTCTGCGCGGAAATGGACGAACAGTGGGGATACGTCG
GGGCTAAATCGCGCCAGCGCTGGCTGTTTTACGCGTATGACAGGCTCCGGAAGACGGTTGTTGCGCACGTATTCGGTGAACGCACTATGGCGACGCTGGG
GCGTCTTATGAGCCTGCTGTCACCCTTTGACGTGGTGATATGGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATC
AGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGG
AGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC
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
276 bp91 aa56331+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

VASVSISCPSCSATDGVVRNGKSTAGHQRYLCSHCRKTWQLQFTYTASQPGTHQKIIDMAMNGVGCRATARIMGVGLNTIFRHLKNSGRSR

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
525 bp174 aa229753+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

YGHEWRWMPGNRPHYGRWPQHDFPPFKKLRPQSVTSRIQPGSDVIVCAEMDEQWGYVGAKSRQRWLFYAYDRLRKTVVAHVFGERTMATLGRLMSLLSPF
DVVIWMTDGWPLYESRLKGKLHVISKRYTQRIERHNLNLRQHLARLGRKSLSFSKSVELHDKVIGHYLNIKHYQ

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
698 bp232 aa56753+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

VASVSISCPSCSATDGVVRNGKSTAGHQRYLCSHCRKTWQLQFTYTASQPGTHQKIIDMAMNGVGCRATARIMGVGLNTIFRHLKKLRPQSVTSRIQPGS
DVIVCAEMDEQWGYVGAKSRQRWLFYAYDRLRKTVVAHVFGERTMATLGRLMSLLSPFDVVIWMTDGWPLYESRLKGKLHVISKRYTQRIERHNLNLRQH
LARLGRKSLSFSKSVELHDKVIGHYLNIKHYQ

 

Blast result :
Comments
IS1 from Ohtsubo and Ohtsubo (1978) was renamed IS1R after Ohtsubo et al. (1981) discovered that there are several IS1 iso-insertion sequences. The 5' and 3' ends of IS1R are approximate inverted repeats. Ohtsubo et al. (1981) found the CDS regions annotated below conserved among several IS1s. Deletion mutations in either of these two coding frames or in the two ends of IS1R cause loss of translocation activity. Three R100 derived small circular plasmids (pSM1, pSM2, pSM5) contain IS1R. pSM2 consists of map units 82.7-89.3 (the 3' end of IS1R) in circularized form. pSM1 is the same as pSM2, except for a deletion of map units 87.4-88.6. pSM 15 consists of map units 83.4-89.3 in circularized form. The general organization of Tn2670 present on R100 is as follows: IS1-Tn21-cat-IS1, with IS1R located 58 bp upstream of Tn21. A transposon similar to the R100 Tn2670 has also been found in Acinetobacter baumannii SAK (Elisha and Steyn, 1991), a gram-negative bacteria causing nozocomial colonization in hospitals. Of the 181-bp determined, 180 were identical.
Additionnal accession number : AF326777 ( Shigella flexneri 2a, 2000). This sequence is 99% DNA, 100% aa (ORF2) and 98% aa (ORF1, mutation at position 44 : T -> X) similar to the sequence of the database.
The third ORF is the probable ORFAB transposase reconstructed in silico by possible -1 frameshift.
References
1] Ohtsubo, H., and Ohtsubo, E. (1978) Proc. Natl. Acad. Sci., USA 75, 615-619.
2] Ohtsubo, H., Nyman, K., Doroszkkiewicz, W., and Ohtsubo, E. (1981) Nature 292, 640-643.
3] Misra, T.K., Brown, N.L., Fritzinger, D.C., Pridmore, R.D., Barnes, W.M., Haberstroh, L., and Silver, S. (1984) Proc. Natl. Acad. Sci., USA 81, 5975-5979.
4] Elisha, B.G., and Steyn, L.M. (1991) Plasmid 25, 96-104.
5] Luck,S.N., Turner,S.A., Rajakumar,K., Sakellaris,H. and Adler,B. (2001) Infect. Immun. 69 (10), 6012-6021