ISfinder

ISKol4

Family IS3
Group IS150

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

Accession number	Transposition	Origin	Host
NC_012785	ND	Kosmotoga olearia	Kosmotoga olearia TBF 19.5.1

DNA section

IS Length : 1474 bp

Ends

IR Length : 29/41

IRL : TGACAATCGACATATTTACCCCCTAAAAGGATTGGACAAAAGAAGCCCAA
IRR : TGGTTCTCGACGGCTTGACCCCCAAATATTGGACAAAAACAGACCAACAT

Insertion site

Left flank	Direct repeat	Right flank	DR Length
AGGTTGTACG		TTAATGTAGG	0

DNA sequence

TGACAATCGACATATTTACCCCCTAAAAGGATTGGACAAAAGAAGCCCAACAGCATAGAATAAAGGAAAGAAAAAGGGGGTAAAAGGAATGAAAGGAAAA
ACACCGCGAAGATACAGTTCAGAATTCAAAATCAAGTTGGTTAAGGAGTATTTAGGAACAAACAAGAGTTACACAGAATTGGGAGTCGAATATGATGTGG
ATGCTTCACTTATCATGAGTTGGGTAAAGCGCTACGAAAGATACAAAGAAAATGCATTCCAGCCTCCGAAAAGGAAGCCTTCATTCATAGCAGATGAAAG
CAAGATACCCGCTTTTCTTAAAGAAGAGCTCGGCCTGGATAAGATAAAGGAACACAGTGATGATCCTGAAGAAATAAACGCCGAATTGGAAAGATTGAAA
TTGGAACTTGCTGAGAGAGACCTGAGAATAAGAATACTCAAGGAAAAATTAAAAAAAACGAACATGGAAGAGAACCAGGGAAAAAAGTAACAGATATTAC
GATCCTCTGTATTGCTAATAAGTACATAAATTGGGGGTTTCGTGTAAGCTTCGTTCTTGAAGTTTTAGAGATACCAAGGAGTAGCTATTACAGGAGCAAG
AATCCGGGCTTTTTCCTGAAAGGCAGGAGAGGAAGAAAGGAAAGAGGTTATGCCTTTAATGTTTTTGGAGGTATCACAAAAGACGAAGAGATAGAAAAAC
TGCTGCTGTGGTTTAATGCGATCGAATCTCCTTTACAAGAGGAATATTATTTGAAGTACATGGGTTCAAAAAAGATAGCCAGATATATCCGGAACGTATA
CGGAATCATAGTAAATCACAAGAAATTGCACCGACTCAGGAAAAAGCTCGGACTTGTTGGGAAGTACAAAAGGCGTGAAAGGCATCCATACACTCGAAGC
CGTTCAATAACAGTGACAAAAGCGAACCAATTGTGGGAAGCGGATATAACATTCGTAAAAACACGTGAAGATGGGAATGCAGCGATACTGAACATAATAG
ACGTGTATGACAGAAGCATAGTGGGAACATATGTAGGTAAAAGCTGCAAAAAGGAACATTTCATTCAATTAATGAAAATAGCGATCACAAAAAGAGCAAA
ACCACAAATAATAAGAACGGATAACGGAAGCCAATTTAAAGCATTAGATACGGGAATATACATGAATGAAGAAAATATAATCCATGAATTTGGAATAGTA
AGGAATCCGGATTCGCAAGCATTTATTGAATCGTCATTCTCTTCTTTGAAAAGGGAATTCGTAAGAAACAACGAATTCAAGAATCTTGAAGACTTGTGTG
AAAAACTAAAGGTATATCTGTCTTTTTACAACAACCTGAGACCTCATGGGTCATTGAAATACCAAACACCAAGATACTATACTGAATTCTCCAGCCAAAA
CGAGCCTGTGTACGTAAATCCTTGATGTTGGTCTGTTTTTGTCCAATATTTGGGGGTCAAGCCGTCGAGAACCA

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
402 bp	133 aa	89	490	+	No

ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MKGKTPRRYSSEFKIKLVKEYLGTNKSYTELGVEYDVDASLIMSWVKRYERYKENAFQPPKRKPSFIADESKIPAFLKEELGLDKIKEHSDDPEEINAEL
ERLKLELAERDLRIRILKEKLKKTNMEENQGKK

Blast result :

ORF 2

Length		Begin	End	Strand	Fusion ORF
1011 bp	336 aa	415	1425	+	No

ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

ERPENKNTQGKIKKNEHGREPGKKVTDITILCIANKYINWGFRVSFVLEVLEIPRSSYYRSKNPGFFLKGRRGRKERGYAFNVFGGITKDEEIEKLLLWF
NAIESPLQEEYYLKYMGSKKIARYIRNVYGIIVNHKKLHRLRKKLGLVGKYKRRERHPYTRSRSITVTKANQLWEADITFVKTREDGNAAILNIIDVYDR
SIVGTYVGKSCKKEHFIQLMKIAITKRAKPQIIRTDNGSQFKALDTGIYMNEENIIHEFGIVRNPDSQAFIESSFSSLKREFVRNNEFKNLEDLCEKLKV
YLSFYNNLRPHGSLKYQTPRYYTEFSSQNEPVYVNP

Blast result :

ORF 3

Length		Begin	End	Strand	Fusion ORF
1337 bp	445 aa	89	1425	+	Yes

ORF function : Transposase
Chemistry : DDE

ORF sequence :

MKGKTPRRYSSEFKIKLVKEYLGTNKSYTELGVEYDVDASLIMSWVKRYERYKENAFQPPKRKPSFIADESKIPAFLKEELGLDKIKEHSDDPEEINAEL
ERLKLELAERDLRIRILKEKLKKTNMEENQGKKVTDITILCIANKYINWGFRVSFVLEVLEIPRSSYYRSKNPGFFLKGRRGRKERGYAFNVFGGITKDE
EIEKLLLWFNAIESPLQEEYYLKYMGSKKIARYIRNVYGIIVNHKKLHRLRKKLGLVGKYKRRERHPYTRSRSITVTKANQLWEADITFVKTREDGNAAI
LNIIDVYDRSIVGTYVGKSCKKEHFIQLMKIAITKRAKPQIIRTDNGSQFKALDTGIYMNEENIIHEFGIVRNPDSQAFIESSFSSLKREFVRNNEFKNL
EDLCEKLKVYLSFYNNLRPHGSLKYQTPRYYTEFSSQNEPVYVNP

Blast result :

Comments

ISKol4 is 46% aa similar to IS1296. The third ORf is a putative ORFAB transposase reconstructed in silico by possible -1 frameshift.

References

1] ISfinder annotation (2009)
2] Lucas,S., Copeland,A., Lapidus,A., Glavina del Rio,T., Tice,H., Bruce,D., Goodwin,L., Pitluck,S., Chertkov,O., Brettin,T., Detter,J.C., Han,C., Schmutz,J., Larimer,F., Land,M., Hauser,L., Kyrpides,N., Ovchinnikova,G. and Noll,K. (2009) Direct submission GenBank.