ISfinder Mirror Site

ISHde1

Family IS630
Group

MGE type ISRelated element(s) :
Isoform Synonym(s)

Accession number	Transposition	Origin	Host
CP001277	ND	Candidatus Hamiltonella	Candidatus Hamiltonella defensa 5AT Acyrthosiphon pisum T5A

DNA section

IS Length : 906 bp

Ends

IR Length : 23/29

IRL : TATAGCTAAGCGATTTAATTTTAGTTACAATATAAAGAACTAATTAGCAT
IRR : TATAGCTAAACGACATAAGAATAGTTACATAATATGTTCTGAAAACAAGG

Insertion site

Left flank	Direct repeat	Right flank	DR Length
TGCCGGCATCGACTCCC	TTA	AGGTAGTAGAGAA	3

DNA sequence

TATAGCTAAGCGATTTAATTTTAGTTACAATATAAAGAACTAATTAGCATGAGGTCACTATGAGTTATTCAGTGGATTTTCGTCAAAAAGTCTTGAGTAT
TCGAGAGAAAGAAGGACTGAGCATCAGAGCAACGGCGAAGCGTTTTCACGTAGGTACAGATACTCTCAGGCGTTGGCTCAAGCGAATAGAACCGAAACCC
TCGGGTCCGCGTCGAGGCAAGATGGATAAAGAGGCGTTTATCAAAGATGTGGCAGAGTATCCAGATAGCTATCAACGGGAACGGGCGGCCCGTTTCGGGG
TGTGCCCCAAAGCCATCTGGCAAGCATTGAAAAGATGGGGTCTGACCTATAAAAAAAACTCTGCGTCATCCCAAGGCAAACGAAGAGGCACGACAGGGGT
TCCAGGAAAAAATCGCGGGGTATCAAAAGCAGGGTAAATCTCTGGTTTATCTCGATGAGAGCGGCTTTGCTCACGATATGCCCCGCCTCTACGGATACGC
TACACGAGGTCAACGCTGTTTTGGGACTCACGATTGGCAGGCTAAGGGCCGCACTAACGTCATTGGTGCCTTATTAGGGGTCACTCTCATCGCGGTGGGC
CTCTTTAACTGCTCCATTAACAGCGATGTTTTTTATGCCTGGGTCACTCAGCTGCTCCTACCCGCTCTTCCTCATCCGTGCGTGATGATGATGGATAACG
CTTCTTTCCACAAGCGAAAAGATATTCAACACGCCATTCTCAACGCCGGTCATTCTATTGAATATTTGCCTCCTTATTCGCCCGAGTTCAACCCTATTGA
GCACACATGGGCTCAAGCTAAAAGAAAAAGAAGAGAACTTCAATGCGACATCAATACCTTGTTTTCAGAACATATTATGTAACTATTCTTATGTCGTTTA
GCTATA

Recoding section

Recoding by frameshift
Frame -1
Type translational
Experimentally demonstrated No

Stimulators :

Shine-Dalgarno sequence :
Secondary structure :

Recoding motif :

Protein section

ORF number : 3

ORF 1

Length		Begin	End	Strand	Fusion ORF
378 bp	125 aa	60	437	+	No

ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MSYSVDFRQKVLSIREKEGLSIRATAKRFHVGTDTLRRWLKRIEPKPSGPRRGKMDKEAFIKDVAEYPDSYQRERAARFGVCPKAIWQALKRWGLTYKKN
SASSQGKRRGTTGVPGKNRGVSKAG

Blast result :

ORF 2

Length		Begin	End	Strand	Fusion ORF
537 bp	146 aa	346	882	+	No

ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

PIKKTLRHPKANEEARQGFQEKIAYQKQGKSLVYLDESGFAHDMPRLYGYATRGQRCFGTHDWQAKGRTNVIGALLGVTLIAVGLFNCSINSDVFYAWVT
QLLLPALPHPCVMMMDNASFHKRKDIQHAILNAGHSIEYLPPYSPEFNPIEHTWAQAKRKRRELQCDINTLFSEHIM

Blast result :

ORF 3

Length		Begin	End	Strand	Fusion ORF
823 bp	272 aa	60	882	+	Yes

ORF function : Transposase
Chemistry : DDE

ORF sequence :

MSYSVDFRQKVLSIREKEGLSIRATAKRFHVGTDTLRRWLKRIEPKPSGPRRGKMDKEAFIKDVAEYPDSYQRERAARFGVCPKAIWQALKRWGLTYKKT
LRHPKANEEARQGFQEKIAYQKQGKSLVYLDESGFAHDMPRLYGYATRGQRCFGTHDWQAKGRTNVIGALLGVTLIAVGLFNCSINSDVFYAWVTQLLLP
ALPHPCVMMMDNASFHKRKDIQHAILNAGHSIEYLPPYSPEFNPIEHTWAQAKRKRRELQCDINTLFSEHIM

Blast result :

Comments

ISHde1 is 55% aa similar to ISOt3.
The third ORF is the putative ORFAB transposase reconstructed by possible -1 frameshift.

References

1] ISfinder submission (2018)
2] Degnan,P.H., Yu,Y., Sisneros,N., Wing,R.A. and Moran,N.A. (2009) Proc. Natl. Acad. Sci. U.S.A. 106 (22), 9063-9068