ISVch4
- Family IS3
- Group IS3
Isoform Synonym(s) IS1359, IS1359Am
| Accession number | Transposition | Origin | Host |
|---|---|---|---|
| NC_002505 | ND | Vibrio cholerae | Vibrio cholerae Amazonia 3509 Vibrio cholerae O1 biovar eltor N16961 |
DNA section
IS Length : 1258 bp
Ends
IR Length : 24/35
IRL : TGTAGTGGCATAGTGAATTTGGTCACTTAGTTAGAGGTGATATCATCACC
IRR : TGTAGTGGTCAACTAAAATTGGCCACGGTTTTAGAGTTTTCCCAATATAA
Insertion site
| Left flank | Direct repeat | Right flank | DR Length |
|---|---|---|---|
| TAAGCTACAAAAACCCA | AAC | TTTGATTTAGGTATGCGTC | 3 |
| CATCTACTAT | ATT | GAGCAGTTAA | 3 |
DNA sequence
TGTAGTGGCATAGTGAATTTGGTCACTTAGTTAGAGGTGATATCATCACCTCATAAGTTAACAGGTGACATTATGACAAAACGTACAAGACGACTATTTA
GCGCAGAATTTAAGTTAGAAGCAGCGCAGCTAGTCTTAGACCAAAATTACTCAGTGACGGAAGCAGCCCAAGCCATGAATGTGGGCAAGTCCACGATGGA
TAAATGGGTTCGCCAGCTTAGAGAAGAACGCCAAGGGAAAACACCTAAAGCTTCACCTATGACCCCTGAGCAAATAGAAATTCGGGAATTGAAAAAGAAG
CTGGCTCGCCTTGAAGAGCATAATGAAATACTAAAAAAAGCCACGGCTCTCTTGATGTCGGACTCACTGAACAATTCTTGATAATCAAGAAACTCAAGCA
GAGCCACAGCGTAAAAATATTATGCGAAGTCTTCAATGTTCATCGAAGTAGTTATCACTATTGGCTTAAACGCCCAGCGTTAATTAATGCGGAAACAATA
AAACTGCGCAGCTTGATTAGCGAGGCTCACGCCGCAAGCAATGGCTCTGCGGGAGCGAGAACCATTGCAGATATAGTCACAAATCAGGGTGTAAAGCTGA
GCCGATACCGAGCAACAAAGCTAATGAGAACTCTTGGTTTAGTAAGCTGCCAAGAACCAAAGCATCGTTACAGAAAGGCTTCACAAGAACATATTGACGT
TCCAAATCACTTAAGTCGTCAATTTGCTGTTACGGCTCCAAATGAAGTCTGGGCTGGCGATGTTACGTATATTTGGACTGGTAATCGGTGGATGTATTTA
GCGGTCGTTATCGATCTTTTTGCCCGCAAAGTGATCGGTTGGTCAATGTCTTTGTCGCCTGATAGTCGGTTGACAGGTAAAGCGCTGTCTATGGCCTATG
AATCTCGCGGAAAGCCAAAAGGTGTCATGTTCCATAGCGATCAAGGCAGTCATTATACTAGCCGTAAATACCGTCAATTACTGTGGCGCTTTCAAATAAA
ACAGAGTTTATCTCGCCGAGGAAACTGTTGGGATAATGCGCCGATAGAGCGCTTCTTTAGAAGTCTGAAGACGGAATGGGTGCCAACTGTGGGTTATCGT
AGCTTCGCTGAGGCTCAACAAGAGATCACCCGCTACATTATCGGATATTACTGCCAACTCAGGCCACATCAGTATAACGGTGGTCTAACTCCCAATGAAT
CAGAACGATTATATTGGGAAAACTCTAAAACCGTGGCCAATTTTAGTTGACCACTACA
GCGCAGAATTTAAGTTAGAAGCAGCGCAGCTAGTCTTAGACCAAAATTACTCAGTGACGGAAGCAGCCCAAGCCATGAATGTGGGCAAGTCCACGATGGA
TAAATGGGTTCGCCAGCTTAGAGAAGAACGCCAAGGGAAAACACCTAAAGCTTCACCTATGACCCCTGAGCAAATAGAAATTCGGGAATTGAAAAAGAAG
CTGGCTCGCCTTGAAGAGCATAATGAAATACTAAAAAAAGCCACGGCTCTCTTGATGTCGGACTCACTGAACAATTCTTGATAATCAAGAAACTCAAGCA
GAGCCACAGCGTAAAAATATTATGCGAAGTCTTCAATGTTCATCGAAGTAGTTATCACTATTGGCTTAAACGCCCAGCGTTAATTAATGCGGAAACAATA
AAACTGCGCAGCTTGATTAGCGAGGCTCACGCCGCAAGCAATGGCTCTGCGGGAGCGAGAACCATTGCAGATATAGTCACAAATCAGGGTGTAAAGCTGA
GCCGATACCGAGCAACAAAGCTAATGAGAACTCTTGGTTTAGTAAGCTGCCAAGAACCAAAGCATCGTTACAGAAAGGCTTCACAAGAACATATTGACGT
TCCAAATCACTTAAGTCGTCAATTTGCTGTTACGGCTCCAAATGAAGTCTGGGCTGGCGATGTTACGTATATTTGGACTGGTAATCGGTGGATGTATTTA
GCGGTCGTTATCGATCTTTTTGCCCGCAAAGTGATCGGTTGGTCAATGTCTTTGTCGCCTGATAGTCGGTTGACAGGTAAAGCGCTGTCTATGGCCTATG
AATCTCGCGGAAAGCCAAAAGGTGTCATGTTCCATAGCGATCAAGGCAGTCATTATACTAGCCGTAAATACCGTCAATTACTGTGGCGCTTTCAAATAAA
ACAGAGTTTATCTCGCCGAGGAAACTGTTGGGATAATGCGCCGATAGAGCGCTTCTTTAGAAGTCTGAAGACGGAATGGGTGCCAACTGTGGGTTATCGT
AGCTTCGCTGAGGCTCAACAAGAGATCACCCGCTACATTATCGGATATTACTGCCAACTCAGGCCACATCAGTATAACGGTGGTCTAACTCCCAATGAAT
CAGAACGATTATATTGGGAAAACTCTAAAACCGTGGCCAATTTTAGTTGACCACTACA
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 | |
|---|---|---|---|---|---|
| 345 bp | 114 aa | 37 | 381 | + | No |
Description : First part of the transposase
ORF sequence :
MISSPHKLTGDIMTKRTRRLFSAEFKLEAAQLVLDQNYSVTEAAQAMNVGKSTMDKWVRQLREERQGKTPKASPMTPEQIEIRELKKKLARLEEHNEILK
KATALLMSDSLNNS
KATALLMSDSLNNS
Blast result :ORF 2
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 924 bp | 307 aa | 327 | 1250 | + | No |
Description : Second part of the transposase
ORF sequence :
NTKKSHGSLDVGLTEQFLIIKKLKQSHSVKILCEVFNVHRSSYHYWLKRPALINAETIKLRSLISEAHAASNGSAGARTIADIVTNQGVKLSRYRATKLM
RTLGLVSCQEPKHRYRKASQEHIDVPNHLSRQFAVTAPNEVWAGDVTYIWTGNRWMYLAVVIDLFARKVIGWSMSLSPDSRLTGKALSMAYESRGKPKGV
MFHSDQGSHYTSRKYRQLLWRFQIKQSLSRRGNCWDNAPIERFFRSLKTEWVPTVGYRSFAEAQQEITRYIIGYYCQLRPHQYNGGLTPNESERLYWENS
KTVANFS
RTLGLVSCQEPKHRYRKASQEHIDVPNHLSRQFAVTAPNEVWAGDVTYIWTGNRWMYLAVVIDLFARKVIGWSMSLSPDSRLTGKALSMAYESRGKPKGV
MFHSDQGSHYTSRKYRQLLWRFQIKQSLSRRGNCWDNAPIERFFRSLKTEWVPTVGYRSFAEAQQEITRYIIGYYCQLRPHQYNGGLTPNESERLYWENS
KTVANFS
Blast result :ORF 3
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 1214 bp | 404 aa | 37 | 1250 | + | Yes |
Chemistry : DDE
ORF sequence :
MISSPHKLTGDIMTKRTRRLFSAEFKLEAAQLVLDQNYSVTEAAQAMNVGKSTMDKWVRQLREERQGKTPKASPMTPEQIEIRELKKKLARLEEHNEILK
KSHGSLDVGLTEQFLIIKKLKQSHSVKILCEVFNVHRSSYHYWLKRPALINAETIKLRSLISEAHAASNGSAGARTIADIVTNQGVKLSRYRATKLMRTL
GLVSCQEPKHRYRKASQEHIDVPNHLSRQFAVTAPNEVWAGDVTYIWTGNRWMYLAVVIDLFARKVIGWSMSLSPDSRLTGKALSMAYESRGKPKGVMFH
SDQGSHYTSRKYRQLLWRFQIKQSLSRRGNCWDNAPIERFFRSLKTEWVPTVGYRSFAEAQQEITRYIIGYYCQLRPHQYNGGLTPNESERLYWENSKTV
ANFS
KSHGSLDVGLTEQFLIIKKLKQSHSVKILCEVFNVHRSSYHYWLKRPALINAETIKLRSLISEAHAASNGSAGARTIADIVTNQGVKLSRYRATKLMRTL
GLVSCQEPKHRYRKASQEHIDVPNHLSRQFAVTAPNEVWAGDVTYIWTGNRWMYLAVVIDLFARKVIGWSMSLSPDSRLTGKALSMAYESRGKPKGVMFH
SDQGSHYTSRKYRQLLWRFQIKQSLSRRGNCWDNAPIERFFRSLKTEWVPTVGYRSFAEAQQEITRYIIGYYCQLRPHQYNGGLTPNESERLYWENSKTV
ANFS
Blast result :
Comments
ISVch4 is 91% (ORFA) and 78% (ORFB) aa similar to IS911. The third ORF is a putative ORFAB reconstructed in silico by possible -1 frameshift.
ISVch4 is part of Genbank entry EU272902 to be released.
ISVch4 is part of Genbank entry EU272902 to be released.
References
1] Figueiredo, S. C. A., Reis, R. C., Gonçalves, M. S. M, Beltrão, P. J. M. S. I., and Coelho, A. (2008) The VPI-2 (Vibrio pathogenicity island-2) of Vibrio cholerae Amazonia: a modular arrangement with insertion sequences and a deletion. Submitted for publication.
2] Heidelberg,J.F., Eisen,J.A., Nelson,W.C., Clayton,R.A., Gwinn,M.L., Dodson,R.J., Haft,D.H., Hickey,E.K., Peterson,J.D., Umayam,L.A., Gill,S.R., Nelson,K.E., Read,T.D., Tettelin,H., Richardson,D., Ermolaeva,M.D., Vamathevan,J., Bass,S., Qin,H., Dragoi,I., Sellers,P., McDonald,L., Utterback,T., Fleishmann,R.D., Nierman,W.C., White,O., Salzberg,S.L., Smith,H.O., Colwell,R.R.,Mekalanos,J.J., Venter,J.C. and Fraser,C.M. (2000) Nature 406 (6795), 477-483
3] Clark,C.A., Purins,L., Kaewrakon,P., Focareta,T. and Manning,P.A. (2000) Microbiology 146 (Pt 10), 2605-2612
2] Heidelberg,J.F., Eisen,J.A., Nelson,W.C., Clayton,R.A., Gwinn,M.L., Dodson,R.J., Haft,D.H., Hickey,E.K., Peterson,J.D., Umayam,L.A., Gill,S.R., Nelson,K.E., Read,T.D., Tettelin,H., Richardson,D., Ermolaeva,M.D., Vamathevan,J., Bass,S., Qin,H., Dragoi,I., Sellers,P., McDonald,L., Utterback,T., Fleishmann,R.D., Nierman,W.C., White,O., Salzberg,S.L., Smith,H.O., Colwell,R.R.,Mekalanos,J.J., Venter,J.C. and Fraser,C.M. (2000) Nature 406 (6795), 477-483
3] Clark,C.A., Purins,L., Kaewrakon,P., Focareta,T. and Manning,P.A. (2000) Microbiology 146 (Pt 10), 2605-2612