ISfinder Mirror Site

ISHwa16

Family IS630
Group

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

Accession number	Transposition	Origin	Host
AM180088	ND	Haloquadratum walsbyi	Haloquadratum walsbyi DSM 16790

DNA section

IS Length : 1066 bp

Ends

IR Length : 9/14

IRL : CTTGACGCCGAAAGTTTTGACACACGGAGGAACCTTGTTTAGGTATGGCC
IRR : CTCACCGACAGAGATACTGATACAATCCGGGCGGATTAATCTCGGTCATC

Insertion site

Left flank	Direct repeat	Right flank	DR Length
ACAGAGAATA	TA	TAAAAACATA	2
GTCTCAACAA	TA	AAGGTGGCTT	2

DNA sequence

CTTGACGCCGAAAGTTTTGACACACGGAGGAACCTTGTTTAGGTATGGCCAAGGACGGGAACAAGATTCCCGATCTTTCAGTTGAGCGCGTCCGCGAGCA
GCTCGCGGACGAGCGTGATCCGAAAGTAATCAAGCGTCTTACTGCTGCACGCGGATATCTCGCTGGGCTATCTCCAGATGGTATTGGGGAAAAATACGGG
TGGCCTCGTCAGACAGTGTACAACTGGTTAGATCGCTTCGAAGAGCGCGACTTTGAAGACGCGCTCTATGACGACGAATGGTCAGGAAGACCACCTGAAC
TCTCTGACGAACAGTTCCACCAGTTTGCTGAAACACTCAACCAATCACCCGAAGAGGCTGGATACGACGTGGCTGCTTGGTCGAGTATACTTGCTCAACA
ACACCTCATATCTGAGTGTGATGTTGCACACTCCCGGCGTCACGTTCAGCGACTAATGAAAGAGGCCGAGGTTTCCTGGAAGAAACCTCGGCCAGAACCA
GCCTCGGCTGATGAGGAAGATCTTGAGCGGGACGACGACGAGCTCAAAAAAAGTCGGGAGACAGGATGAAGACAGACTGGTCGTAACGATTGATCAGTTC
AGGAAATCGATTGGAGCTGATCTCAGATATGCGTGGTTTCCGATTGACGAGAGGCCGACAGTGAACGTGTCGGCCTCTCGCGATGGAATCAATTTCTTGG
GCGGTCTCACCGAGGACAGTGAGATACTGTTTTTGGAATGCGCTGGTTCGTTCATCAAGGAAACAACGGTTCGATTTCTCCAGTCACTTCAGGCAAGATT
CGGAGAGAAGCTGCTCGTGGTTCTCGACAAGGGTTTCTATTTCACAGCGAAGAAAGTCAAAGAATTTGCCGAGAAACCGAATCCAGAGCTTCTATATCTC
CCGACTGGGATGGCTAAGCTGAACCCAACCGAAGAGTGTTGGCGGCAACTCAGATCAGCTCTTGGTAATCAGTACTTTGGAGAAATTGACGAACTTCGAA
GTGAGATCCGCTCAGCGATGACCGAGATTAATCCGCCCGGATTGTATCAGTATCTCTGTCGGTGAG

Recoding section

Recoding by frameshift
Frame
Type
Experimentally demonstrated

Stimulators :

Shine-Dalgarno sequence :
Secondary structure :

Recoding motif :

Protein section

ORF number : 3

ORF 1

Length		Begin	End	Strand	Fusion ORF
525 bp	174 aa	45	569	+	No

ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MAKDGNKIPDLSVERVREQLADERDPKVIKRLTAARGYLAGLSPDGIGEKYGWPRQTVYNWLDRFEERDFEDALYDDEWSGRPPELSDEQFHQFAETLNQ
SPEEAGYDVAAWSSILAQQHLISECDVAHSRRHVQRLMKEAEVSWKKPRPEPASADEEDLERDDDELKKSRETG

Blast result :

ORF 2

Length		Begin	End	Strand	Fusion ORF
606 bp	201 aa	460	1065	+	No

ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

KRPRFPGRNLGQNQPRLMRKILSGTTTSSKKVGRQDEDRLVVTIDQFRKSIGADLRYAWFPIDERPTVNVSASRDGINFLGGLTEDSEILFLECAGSFIK
ETTVRFLQSLQARFGEKLLVVLDKGFYFTAKKVKEFAEKPNPELLYLPTGMAKLNPTEECWRQLRSALGNQYFGEIDELRSEIRSAMTEINPPGLYQYLC
R

Blast result :

ORF 3

Length		Begin	End	Strand	Fusion ORF
1021 bp	339 aa	45	1065	+	Yes

ORF function : Transposase
Chemistry : DDE

ORF sequence :

MAKDGNKIPDLSVERVREQLADERDPKVIKRLTAARGYLAGLSPDGIGEKYGWPRQTVYNWLDRFEERDFEDALYDDEWSGRPPELSDEQFHQFAETLNQ
SPEEAGYDVAAWSSILAQQHLISECDVAHSRRHVQRLMKEAEVSWKKPRPEPASADEEDLERDDDELKKVGRQDEDRLVVTIDQFRKSIGADLRYAWFPI
DERPTVNVSASRDGINFLGGLTEDSEILFLECAGSFIKETTVRFLQSLQARFGEKLLVVLDKGFYFTAKKVKEFAEKPNPELLYLPTGMAKLNPTEECWR
QLRSALGNQYFGEIDELRSEIRSAMTEINPPGLYQYLCR

Blast result :

Comments

ISHwa16 is 43% aa suimilar to ISDge17.
The third ORF is a putative ORFAB transposase reconstructed in silico by a possible +1 frameshift, probably reflecting ribosomal slippage.
The integration sites are from two different strains of Haloquadratum walsbyi, HBSQ001 and C23.
Additionnal accession number : FR746099.

References

1] Bolhuis, H., Palm, P., Wende, A., Falb, M., Rampp, M., Rodriguez-Valera, F., Pfeiffer, F., and Oesterhelt, D. (2006) BMC Genomics 7, 169.
2] Dyall-Smith,M.L., Pfeiffer,F., Klee,K., Palm,P., Gross,K., Schuster,S.C., Rampp, M., and Oesterhelt,D. (2011) PLoS One 6: e20968