ISfinder

ISVsa11

Family IS3
Group IS3

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

Accession number	Transposition	Origin	Host
NC_011312	ND	Aliivibrio salmonicida	Aliivibrio salmonicida LFI1238 chromosome 1

DNA section

IS Length : 1258 bp

Ends

IR Length : 27/36

IRL : TGAAGTGGCATAGTAAATTTGGCCACCTAGTTAGAGGTGATATCATCACC
IRR : TGAAGTGGTCAAGTAAAACTGGCCACGGCTTTAGAGTTTAACCAGAAGAT

Insertion site

Left flank	Direct repeat	Right flank	DR Length
AGAAAGCTTA		ATTTCCTTGT	0

DNA sequence

TGAAGTGGCATAGTAAATTTGGCCACCTAGTTAGAGGTGATATCATCACCTCATAGGTTAACAGGTAGCATTATGACTAAACGTATAAGACGATTATTTA
GCACTGAATTTAAACTAGAAGCAGCTCAGCTGGTTCTTGACCAAAATCACTCTGTCGCTGAAGTAGCTAAAGCAATGAATGTCGGTAAATCAACAATGGA
TAAATGGGTTCGACAACTAAAAAATGAACGATTAGGAAAATCTCCCAAAGAATCCCCCATAACTCCAGAGCAAATTGAAATTCGGGAATTGAAAAAGAAA
TTAGCTCGTTTAGAAGAGCATAATTCAATACTAAAAAAGGCTACGGCTCTGTTGATGTCAGACTCCTTGAACAATTCGCATTAATCGAAAAACTCAAGCA
GAGCTATAGTATTAGCATTATTTGTAAAGTATTCGATATCCATCGAAGTAGTTATAAATATTGGCGAGAGCACCTTAAGGAGATGATCGCAGAGCAGGTC
ATATTACGGAGTGAGGTTCGAGCTGCGCATACTGCAAGGAATGGCTCCGCCGGGGCAAGAAGCATTGCCGATATTCTGACAAACAAAGGGATTAAACTGA
GTCGCTATCGTGCATCTAAGTTAATGAAAGAATTAGAGATAGTCAGTTGCCAAATACCAAAGCATAAATACAATAATGAAGTGAAAGAGCACATTGAGAT
ACCAAACAAACTTAACCGAAAATTTGCAGCTACTGCACCAAACAAAGTTTGGTGTGGTGATGTAACTTATATTTGGATAGGCTCTCGATGGGCTTATTTA
GCCATCGTAATGGATTTATTCTCTCGTAAACCGATTGGATGGGCGATGTCATTATCACCTGATAGTACATTGACAGGTAAAGCATTGAGCATGGCCTTTG
AATCAAGAGGAAGACCGAAAAATGTGATGTTTCATTCAGATCAAGGTTGTCATTATACTAGCCGACAATTTAGGCAATTATTATGGCGGTATCAAATAGA
CCAAAGTTTATCTCGTAGAGGAAACTGCTGGGATAATAGTCCAATGGAGCGCTTCTTTCGAAGCTTAAAAAGTGAGTGGATATCGAAAGTCGGATATCGT
AATGTTGTGGAAGCAAAAATAAATATAATTAATTACATTACAAGTTATTACAGTACAGTCAGGCCGCATCAATATAACGGAGGACTAACACCTAATGAAT
CAGAACGGATCTTCTGGTTAAACTCTAAAGCCGTGGCCAGTTTTACTTGACCACTTCA

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
312 bp	103 aa	73	384	+	No

ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MTKRIRRLFSTEFKLEAAQLVLDQNHSVAEVAKAMNVGKSTMDKWVRQLKNERLGKSPKESPITPEQIEIRELKKKLARLEEHNSILKKATALLMSDSLN
NSH

Blast result :

ORF 2

Length		Begin	End	Strand	Fusion ORF
927 bp	308 aa	324	1250	+	No

ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

FNTKKGYGSVDVRLLEQFAMIEKLKQSYSISIICKVFDIHRSSYKYWREHLKEMIAEQVILRSEVRAAHTARNGSAGARSIADILTNKGIKLSRYRASKL
MKELEIVSCQIPKHKYNNEVKEHIEIPNKLNRKFAATAPNKVWCGDVTYIWIGSRWAYLAIVMDLFSRKPIGWAMSLSPDSTLTGKALSMAFESRGRPKN
VMFHSDQGCHYTSRQFRQLLWRYQIDQSLSRRGNCWDNSPMERFFRSLKSEWISKVGYRNVVEAKINIINYITSYYSTVRPHQYNGGLTPNESERIFWLN
SKAVASFT

Blast result :

ORF 3

Length		Begin	End	Strand	Fusion ORF
1178 bp	392 aa	73	1250	+	Yes

ORF function : Transposase
Chemistry : DDE

ORF sequence :

MTKRIRRLFSTEFKLEAAQLVLDQNHSVAEVAKAMNVGKSTMDKWVRQLKNERLGKSPKESPITPEQIEIRELKKKLARLEEHNSILKKGYGSVDVRLLE
QFAMIEKLKQSYSISIICKVFDIHRSSYKYWREHLKEMIAEQVILRSEVRAAHTARNGSAGARSIADILTNKGIKLSRYRASKLMKELEIVSCQIPKHKY
NNEVKEHIEIPNKLNRKFAATAPNKVWCGDVTYIWIGSRWAYLAIVMDLFSRKPIGWAMSLSPDSTLTGKALSMAFESRGRPKNVMFHSDQGCHYTSRQF
RQLLWRYQIDQSLSRRGNCWDNSPMERFFRSLKSEWISKVGYRNVVEAKINIINYITSYYSTVRPHQYNGGLTPNESERIFWLNSKAVASFT

Blast result :

Comments

ISVsa11 is 83% aa similar to ISVch4. The third ORF is a putative ORFAB transposase reconstructed in silico by possible -1 frameshift.

References

1] ISfinder annotation (2009)
2] Hjerde,E., Lorentzen,M.S., Holden,M.T.G., Seeger,K., Paulsen,S., Bason,N., Churcher,C., Harris,D., Norbertczak,H., Quail,M.A., Sanders,S., Thurston,S., Parkhill,J., Willassen,N.P. and Thomson,N.R. (2008) Direct submission GenBank.