ISPsy13
- Family IS3
- Group IS3
Isoform Synonym(s)
| Accession number | Transposition | Origin | Host |
|---|---|---|---|
| AE016853 | ND | Pseudomonas syringae | Pseudomonas syringae DC3000 |
DNA section
IS Length : 1232 bp
Ends
IR Length : 20/26
IRL : TGTACTGGTCTAATGATTCCGGACACTCACTTAGGCAAGAATGTCGCCAG
IRR : TGTAATGGTCAACGGATCCCGAACACGACGTTAAGGTTTTCTCGTACTGA
Insertion site
| Left flank | Direct repeat | Right flank | DR Length |
|---|---|---|---|
| GATACGCAAT | ATT | TTCGACTCAA | 3 |
DNA sequence
TGTACTGGTCTAATGATTCCGGACACTCACTTAGGCAAGAATGTCGCCAGATAGAGGTGTCTGAGGACAAAACAACGCCGTACCTTCTCCACTGAATTCA
AGCGCGAGGCCGCAGGCCTCGTGCTCGATCAAGGCTATAGCCATATCGAAGCCGCCCGCTCGCTCGGGGTGGTGGAATCTGCGCTGCGTCGCTGGGTGAG
CCAGCTCCAGCAGGAGCGCAATGGCGTAACGCCCCAGAGCAAAGCCCTGACGCCCGAGCAGCAGAAAATTCAAGAGCAGGAAGCCCGGATCGCTCGCCTT
GAGCGGGAGAAATCCATTTTAAAAATGGCCAACGCGCTCTTGATGTCGGAAGAGCACGAGCGCATGCGCTGATCGATCAGCTCAGTGCCATGAGCCGATC
GAGTTGCCGTGCGAAGTGTTCGAGATACCTCGCTCATGCTACTACGACCATTGCTTGCGACGCCGGTCCACCAACTCCGAACTGGTGCGGCTACGCGGGC
GGTTCAATGAGCTGTTTACACAAAGTCGAAGCGCTGCTGGCAGCCGCAGTATTGTGTCGTTGATGCAGGAAGATAGCGAGCAAATCGGTCGGTTCAAGGT
GCGTGGCCTGATGCGGGAACTGGGATTAATCAGCAAGCAACCGGGCTCGCATGATTACAAAAAAGCAACAGTGGAGCGACCTGACATTCCGAACATTTTG
AATCGGGAGTTCGATGTAACCGCGCCCAATCAGGTCTGGTGTGGCGACATCACCTACATCTGGGCGCAAGGAAAATGGCATTACCTGGCGGTGGTTATGG
ATCTTTATGCGCGTCGGGTGCTGGGCTGGGCGTTTTCAAAAAAATCGGATACGGACTTGGTGATCAAGGCGCTGGACATGGCTTATGAGCAACGCGGCAA
GCCTCAGGGCCTGCTGTTTCATTCGGACCAGGGCGCCCAATACGGTAGCCGACAGTTTCGCAAGCGGCTTTGGCGATATCGCGTGCGCCAGAGCATGAGT
CGCCGAGGTAATTGCTACGACAACTCGCCGATGGCGCGTGTATTCCGCAGCTTGAAAACCGAGTGGATACCCGCCGTGGGCTACATGACGGCCCAAGAGG
CACAAGGGGATATTAGTCATTATCTGATGCATCGCTACAACCGGGTTCGGCCACACCAGTTCAATGATGGACTGGCGCCCGCTCAGTACGAGAAAACCTT
AACGTCGTGTTCGGGATCCGTTGACCATTACA
AGCGCGAGGCCGCAGGCCTCGTGCTCGATCAAGGCTATAGCCATATCGAAGCCGCCCGCTCGCTCGGGGTGGTGGAATCTGCGCTGCGTCGCTGGGTGAG
CCAGCTCCAGCAGGAGCGCAATGGCGTAACGCCCCAGAGCAAAGCCCTGACGCCCGAGCAGCAGAAAATTCAAGAGCAGGAAGCCCGGATCGCTCGCCTT
GAGCGGGAGAAATCCATTTTAAAAATGGCCAACGCGCTCTTGATGTCGGAAGAGCACGAGCGCATGCGCTGATCGATCAGCTCAGTGCCATGAGCCGATC
GAGTTGCCGTGCGAAGTGTTCGAGATACCTCGCTCATGCTACTACGACCATTGCTTGCGACGCCGGTCCACCAACTCCGAACTGGTGCGGCTACGCGGGC
GGTTCAATGAGCTGTTTACACAAAGTCGAAGCGCTGCTGGCAGCCGCAGTATTGTGTCGTTGATGCAGGAAGATAGCGAGCAAATCGGTCGGTTCAAGGT
GCGTGGCCTGATGCGGGAACTGGGATTAATCAGCAAGCAACCGGGCTCGCATGATTACAAAAAAGCAACAGTGGAGCGACCTGACATTCCGAACATTTTG
AATCGGGAGTTCGATGTAACCGCGCCCAATCAGGTCTGGTGTGGCGACATCACCTACATCTGGGCGCAAGGAAAATGGCATTACCTGGCGGTGGTTATGG
ATCTTTATGCGCGTCGGGTGCTGGGCTGGGCGTTTTCAAAAAAATCGGATACGGACTTGGTGATCAAGGCGCTGGACATGGCTTATGAGCAACGCGGCAA
GCCTCAGGGCCTGCTGTTTCATTCGGACCAGGGCGCCCAATACGGTAGCCGACAGTTTCGCAAGCGGCTTTGGCGATATCGCGTGCGCCAGAGCATGAGT
CGCCGAGGTAATTGCTACGACAACTCGCCGATGGCGCGTGTATTCCGCAGCTTGAAAACCGAGTGGATACCCGCCGTGGGCTACATGACGGCCCAAGAGG
CACAAGGGGATATTAGTCATTATCTGATGCATCGCTACAACCGGGTTCGGCCACACCAGTTCAATGATGGACTGGCGCCCGCTCAGTACGAGAAAACCTT
AACGTCGTGTTCGGGATCCGTTGACCATTACA
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 | |
|---|---|---|---|---|---|
| 252 bp | 83 aa | 121 | 372 | + | No |
Description : First part of the transposase
ORF sequence :
MLDQGYSHIEAARSLGVVESALRRWVSQLQQERNGVTPQSKALTPEQQKIQEQEARIARLEREKSILKMANALLMSEEHERMR
Blast result :ORF 2
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 930 bp | 310 aa | 303 | 1232 | + | No |
Description : Second part of the transposase
ORF sequence :
AGEIHFKNGQRALDVGRARAHALIDQLSAMEPIELPCEVFEIPRSCYYDHCLRRRSTNSELVRLRGRFNELFTQSRSAAGSRSIVSLMQEDSEQIGRFKV
RGLMRELGLISKQPGSHDYKKATVERPDIPNILNREFDVTAPNQVWCGDITYIWAQGKWHYLAVVMDLYARRVLGWAFSKKSDTDLVIKALDMAYEQRGK
PQGLLFHSDQGAQYGSRQFRKRLWRYRVRQSMSRRGNCYDNSPMARVFRSLKTEWIPAVGYMTAQEAQGDISHYLMHRYNRVRPHQFNDGLAPAQYEKTL
TSCSGSVDHY
RGLMRELGLISKQPGSHDYKKATVERPDIPNILNREFDVTAPNQVWCGDITYIWAQGKWHYLAVVMDLYARRVLGWAFSKKSDTDLVIKALDMAYEQRGK
PQGLLFHSDQGAQYGSRQFRKRLWRYRVRQSMSRRGNCYDNSPMARVFRSLKTEWIPAVGYMTAQEAQGDISHYLMHRYNRVRPHQFNDGLAPAQYEKTL
TSCSGSVDHY
Blast result :ORF 3
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 1112 bp | 371 aa | 121 | 1232 | + | Yes |
Chemistry : DDE
ORF sequence :
MLDQGYSHIEAARSLGVVESALRRWVSQLQQERNGVTPQSKALTPEQQKIQEQEARIARLEREKSILKNGQRALDVGRARAHALIDQLSAMEPIELPCEV
FEIPRSCYYDHCLRRRSTNSELVRLRGRFNELFTQSRSAAGSRSIVSLMQEDSEQIGRFKVRGLMRELGLISKQPGSHDYKKATVERPDIPNILNREFDV
TAPNQVWCGDITYIWAQGKWHYLAVVMDLYARRVLGWAFSKKSDTDLVIKALDMAYEQRGKPQGLLFHSDQGAQYGSRQFRKRLWRYRVRQSMSRRGNCY
DNSPMARVFRSLKTEWIPAVGYMTAQEAQGDISHYLMHRYNRVRPHQFNDGLAPAQYEKTLTSCSGSVDHY
FEIPRSCYYDHCLRRRSTNSELVRLRGRFNELFTQSRSAAGSRSIVSLMQEDSEQIGRFKVRGLMRELGLISKQPGSHDYKKATVERPDIPNILNREFDV
TAPNQVWCGDITYIWAQGKWHYLAVVMDLYARRVLGWAFSKKSDTDLVIKALDMAYEQRGKPQGLLFHSDQGAQYGSRQFRKRLWRYRVRQSMSRRGNCY
DNSPMARVFRSLKTEWIPAVGYMTAQEAQGDISHYLMHRYNRVRPHQFNDGLAPAQYEKTLTSCSGSVDHY
Blast result :
Comments
There is 1 copy of ISPsy13 in the chromosome of this strain. ISPsy13 and ISPsy12 are closely related but different.
ISPsy13 is 84% aa similar to IS222. The third ORF is the putative ORFAB transposase reconstructed in silico by possible -1 frameshift.
There is no STOP codon for ORFB (and ORFAB) before the end of the IS, the ORF was truncated in silico at the end of th IS.
ISPsy13 is 84% aa similar to IS222. The third ORF is the putative ORFAB transposase reconstructed in silico by possible -1 frameshift.
There is no STOP codon for ORFB (and ORFAB) before the end of the IS, the ORF was truncated in silico at the end of th IS.
References
1] ISfinder submission (2002)
2] Buell,C.R., Joardar,V., Lindeberg,M., Selengut,J., Paulsen,I.T., Gwinn,M.L., Dodson,R.J., Deboy,R.T., Durkin,A.S., Kolonay,J.F., Madupu,R., Daugherty,S., Brinkac,L., Beanan,M.J., Haft,D.H., Nelson,W.C., Davidsen,T., Zafar,N., Zhou,L., Liu,J., Yuan,Q., Khouri,H., Fedorova,N., Tran,B., Russell,D., Berry,K., Utterback,T., Van Aken,S.E., Feldblyum,T.V., D'Ascenzo,M., Deng,W.L., Ramos,A.R., Alfano,J.R., Cartinhour,S., Chatterjee,A.K., Delaney,T.P., Lazarowitz,S.G., Martin,G.B., Schneider,D.J., Tang,X., Bender,C.L., White,O., Fraser,C.M. and Collmer,A. (2003) Proc. Natl. Acad. Sci. U.S.A. 100 (18), 10181-10186.
2] Buell,C.R., Joardar,V., Lindeberg,M., Selengut,J., Paulsen,I.T., Gwinn,M.L., Dodson,R.J., Deboy,R.T., Durkin,A.S., Kolonay,J.F., Madupu,R., Daugherty,S., Brinkac,L., Beanan,M.J., Haft,D.H., Nelson,W.C., Davidsen,T., Zafar,N., Zhou,L., Liu,J., Yuan,Q., Khouri,H., Fedorova,N., Tran,B., Russell,D., Berry,K., Utterback,T., Van Aken,S.E., Feldblyum,T.V., D'Ascenzo,M., Deng,W.L., Ramos,A.R., Alfano,J.R., Cartinhour,S., Chatterjee,A.K., Delaney,T.P., Lazarowitz,S.G., Martin,G.B., Schneider,D.J., Tang,X., Bender,C.L., White,O., Fraser,C.M. and Collmer,A. (2003) Proc. Natl. Acad. Sci. U.S.A. 100 (18), 10181-10186.