ISStma2
- Family IS3
- Group IS150
Isoform Synonym(s)
Accession number | Transposition | Origin | Host |
---|---|---|---|
NC_011071 | ND | Stenotrophomonas maltophilia | Stenotrophomonas maltophilia K279a Stenotrophomonas maltophilia R551-3 |
DNA section
IS Length : 1428 bp
Ends
IR Length : 22/24
IRL : CCTGAAGTGACCCCCGGGAATTGGACACCAGATCCAACCCCGAGGGATAC
IRR : TGAAGTGACCCCCGAGACTTGGACGGGGTCAGGCGGCCGATTGGGCCTGC
Insertion site
Left flank | Direct repeat | Right flank | DR Length |
---|---|---|---|
CAAGCCCCCA | GGG | ACGGGTTCAC | 3 |
CGTGAACCCG | TCC | ATGGGGGCTT | 3 |
GTAAACCCGT | CCC | TGGGGGCTTG | 3 |
GTAAACCCGT | CCC | TGGGGGCTTG | 3 |
GTGAACCCGT | CCA | TGGGGGCTTG | 3 |
GTAAACCCGT | CCT | TGGGGGCTTG | 3 |
GTAAACCCAT | CCC | TGGGGGCTCG | 3 |
DNA sequence
TGAAGTGACCCCCGGGAATTGGACACCAGATCCAACCCCGAGGGATACATGAACAGATACGACGCGCGTTTCAAACTGCAGGTCGCCAAAGAGGCCTGCA
AGACCTCCACATCGGTCAAAGCCATTGCCCGTCGCCACGGCCTGGAGTTCTCCACGGTCAGGCGCTGGGTGGCGACCTATCGGCTGCATGGTTGGCGAGG
ATTTCATCGCCAGGCCCGGTTCTATGACCTCCCGTTCAAGCTGGCTGTCCTGGAGAAAATGAGCCAGGACGGCATGTCCGGGCGGGAGGCCACCACCTAC
TTTCAAATTGGCGATGCCGGCGCGGTGGGGCGATGGCGGCGCCTGTATGCTCAAGGCGGTGCCCAAGCGTTGGCACCCCCTCCGCCGCCGCCCCGAAAGC
CGATGAAAAAGACCCGTTCGTCCAAGCCACCTGAAGATATGAGCCGCGATGAGCTGCTCAAGGAAGTCGCCTATCTGCGTGCGGAGACCGACTACCTAAA
AAAACTCGATGCCTTGATCCGGGAAGAGCAGGCGGCGCAGGACGCAAAGCGCAAGCCGTCCAAGGATTGAGGCAGGTTCATACGCTGTCGCTTCTGCTCG
AAGCAGCTGAGCTGTCACGCAGTACGTTCTATTACCAGAACCATGTCCTGGCCCATCCGGATCAGGACGAGGCACAGCTGTGCGAGCGCATCCGTGCAAT
CTACGATCAAAGCCAAGGGCGCTATGGCTATCGCACGGTGACGCTGGAATTAGCCAATCAGGGCCATCGGACCAATCACAAGCGGGTTCAGCGCCTGATG
GGGGAGATGGGGCTGAAATCGCGGGTGCGTGTGAAGCGCTACCAGGCCTTCAAGGGGGCGGCCAACGTTGTGGTTGGCAATGACCTCAATCGCCAGTTCC
ATGCCGAGCGCCCCAACCAGAAATGGGTGACTGACGTGACCGAGTTCAAGGTGCAGGGCATGAAGCTGTACCTGTCGCCGATCATGGACCTCTACAACGG
CGAAATCGTGGCTTATCAGATCAAGCGTCGGCCCGTATTTGATCTGGTGGGCCAAATGCTGGAGGAGGCCATCAAGAAGCTTCCCCCGGATGAGCGCCCC
ATGATCCACTCCGACCAGGGCTGGCAGTACCAGCATGAAAACTACCGGCACATGCTGGAAAAGCACTCGTTGAAACAAAGCATGTCCCGGCGCGGCAACT
GCCTGGACAATGCGGCGATGGAGAGCTTCTTTGGGACGCTGAAGTCGGAATTCTTCTACCTGAACAGCTTTGACAGCATCGAGAGTCTGGAAGCTGGGCT
GGTGGAATACATCCAGTACTACAACGAAGAGCGCATCAAACTGAAACTGAAAGGTCTCAGCCCGATAAAGTACCGGGAGCAGGCCCAATCGGCCGCCTGA
CCCCGTCCAAGTCTCGGGGGTCACTTCA
AGACCTCCACATCGGTCAAAGCCATTGCCCGTCGCCACGGCCTGGAGTTCTCCACGGTCAGGCGCTGGGTGGCGACCTATCGGCTGCATGGTTGGCGAGG
ATTTCATCGCCAGGCCCGGTTCTATGACCTCCCGTTCAAGCTGGCTGTCCTGGAGAAAATGAGCCAGGACGGCATGTCCGGGCGGGAGGCCACCACCTAC
TTTCAAATTGGCGATGCCGGCGCGGTGGGGCGATGGCGGCGCCTGTATGCTCAAGGCGGTGCCCAAGCGTTGGCACCCCCTCCGCCGCCGCCCCGAAAGC
CGATGAAAAAGACCCGTTCGTCCAAGCCACCTGAAGATATGAGCCGCGATGAGCTGCTCAAGGAAGTCGCCTATCTGCGTGCGGAGACCGACTACCTAAA
AAAACTCGATGCCTTGATCCGGGAAGAGCAGGCGGCGCAGGACGCAAAGCGCAAGCCGTCCAAGGATTGAGGCAGGTTCATACGCTGTCGCTTCTGCTCG
AAGCAGCTGAGCTGTCACGCAGTACGTTCTATTACCAGAACCATGTCCTGGCCCATCCGGATCAGGACGAGGCACAGCTGTGCGAGCGCATCCGTGCAAT
CTACGATCAAAGCCAAGGGCGCTATGGCTATCGCACGGTGACGCTGGAATTAGCCAATCAGGGCCATCGGACCAATCACAAGCGGGTTCAGCGCCTGATG
GGGGAGATGGGGCTGAAATCGCGGGTGCGTGTGAAGCGCTACCAGGCCTTCAAGGGGGCGGCCAACGTTGTGGTTGGCAATGACCTCAATCGCCAGTTCC
ATGCCGAGCGCCCCAACCAGAAATGGGTGACTGACGTGACCGAGTTCAAGGTGCAGGGCATGAAGCTGTACCTGTCGCCGATCATGGACCTCTACAACGG
CGAAATCGTGGCTTATCAGATCAAGCGTCGGCCCGTATTTGATCTGGTGGGCCAAATGCTGGAGGAGGCCATCAAGAAGCTTCCCCCGGATGAGCGCCCC
ATGATCCACTCCGACCAGGGCTGGCAGTACCAGCATGAAAACTACCGGCACATGCTGGAAAAGCACTCGTTGAAACAAAGCATGTCCCGGCGCGGCAACT
GCCTGGACAATGCGGCGATGGAGAGCTTCTTTGGGACGCTGAAGTCGGAATTCTTCTACCTGAACAGCTTTGACAGCATCGAGAGTCTGGAAGCTGGGCT
GGTGGAATACATCCAGTACTACAACGAAGAGCGCATCAAACTGAAACTGAAAGGTCTCAGCCCGATAAAGTACCGGGAGCAGGCCCAATCGGCCGCCTGA
CCCCGTCCAAGTCTCGGGGGTCACTTCA
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 | |
---|---|---|---|---|---|
522 bp | 173 aa | 49 | 570 | + | No |
Description : First part of the transposase
ORF sequence :
MNRYDARFKLQVAKEACKTSTSVKAIARRHGLEFSTVRRWVATYRLHGWRGFHRQARFYDLPFKLAVLEKMSQDGMSGREATTYFQIGDAGAVGRWRRLY
AQGGAQALAPPPPPPRKPMKKTRSSKPPEDMSRDELLKEVAYLRAETDYLKKLDALIREEQAAQDAKRKPSKD
AQGGAQALAPPPPPPRKPMKKTRSSKPPEDMSRDELLKEVAYLRAETDYLKKLDALIREEQAAQDAKRKPSKD
Blast result :ORF 2
Length | Begin | End | Strand | Fusion ORF | |
---|---|---|---|---|---|
948 bp | 315 aa | 453 | 1400 | + | No |
Description : Second part of the transposase
ORF sequence :
AAQGSRLSACGDRLPKKTRCLDPGRAGGAGRKAQAVQGLRQVHTLSLLLEAAELSRSTFYYQNHVLAHPDQDEAQLCERIRAIYDQSQGRYGYRTVTLEL
ANQGHRTNHKRVQRLMGEMGLKSRVRVKRYQAFKGAANVVVGNDLNRQFHAERPNQKWVTDVTEFKVQGMKLYLSPIMDLYNGEIVAYQIKRRPVFDLVG
QMLEEAIKKLPPDERPMIHSDQGWQYQHENYRHMLEKHSLKQSMSRRGNCLDNAAMESFFGTLKSEFFYLNSFDSIESLEAGLVEYIQYYNEERIKLKLK
GLSPIKYREQAQSAA
ANQGHRTNHKRVQRLMGEMGLKSRVRVKRYQAFKGAANVVVGNDLNRQFHAERPNQKWVTDVTEFKVQGMKLYLSPIMDLYNGEIVAYQIKRRPVFDLVG
QMLEEAIKKLPPDERPMIHSDQGWQYQHENYRHMLEKHSLKQSMSRRGNCLDNAAMESFFGTLKSEFFYLNSFDSIESLEAGLVEYIQYYNEERIKLKLK
GLSPIKYREQAQSAA
Blast result :ORF 3
Length | Begin | End | Strand | Fusion ORF | |
---|---|---|---|---|---|
1352 bp | 450 aa | 49 | 1400 | + | Yes |
Chemistry : DDE
ORF sequence :
MNRYDARFKLQVAKEACKTSTSVKAIARRHGLEFSTVRRWVATYRLHGWRGFHRQARFYDLPFKLAVLEKMSQDGMSGREATTYFQIGDAGAVGRWRRLY
AQGGAQALAPPPPPPRKPMKKTRSSKPPEDMSRDELLKEVAYLRAETDYLKKTRCLDPGRAGGAGRKAQAVQGLRQVHTLSLLLEAAELSRSTFYYQNHV
LAHPDQDEAQLCERIRAIYDQSQGRYGYRTVTLELANQGHRTNHKRVQRLMGEMGLKSRVRVKRYQAFKGAANVVVGNDLNRQFHAERPNQKWVTDVTEF
KVQGMKLYLSPIMDLYNGEIVAYQIKRRPVFDLVGQMLEEAIKKLPPDERPMIHSDQGWQYQHENYRHMLEKHSLKQSMSRRGNCLDNAAMESFFGTLKS
EFFYLNSFDSIESLEAGLVEYIQYYNEERIKLKLKGLSPIKYREQAQSAA
AQGGAQALAPPPPPPRKPMKKTRSSKPPEDMSRDELLKEVAYLRAETDYLKKTRCLDPGRAGGAGRKAQAVQGLRQVHTLSLLLEAAELSRSTFYYQNHV
LAHPDQDEAQLCERIRAIYDQSQGRYGYRTVTLELANQGHRTNHKRVQRLMGEMGLKSRVRVKRYQAFKGAANVVVGNDLNRQFHAERPNQKWVTDVTEF
KVQGMKLYLSPIMDLYNGEIVAYQIKRRPVFDLVGQMLEEAIKKLPPDERPMIHSDQGWQYQHENYRHMLEKHSLKQSMSRRGNCLDNAAMESFFGTLKS
EFFYLNSFDSIESLEAGLVEYIQYYNEERIKLKLKGLSPIKYREQAQSAA
Blast result :
Comments
ISStma2 is 66% aa similar to ISBcen9. The third ORF is a putative ORFAB transposase reconstructed in silico by possible -1 frameshift.
There are 3 copies in Stenotrophomonas maltophilia R551-3 and 4 full copies and one partial in Stenotrophomonas maltophilia K279a.
There are 3 copies in Stenotrophomonas maltophilia R551-3 and 4 full copies and one partial in Stenotrophomonas maltophilia K279a.
References
1] Miriam Land (2009) Direct submission
2] Lucas,S., Copeland,A., Lapidus,A., Glavina del Rio,T., Dalin,E., Tice,H., Pitluck,S., Chain,P., Malfatti,S., Shin,M., Vergez,L., Lang,D., Schmutz,J., Larimer,F., Land,M., Hauser,L., Kyrpides,N., Mikhailova,N., Taghavi,S., Monchy,S., Newman,L., Vangronsveld,J., van der Lelie,D. and Richardson,P. (2008) Direct submission GenBank.
3] Crossman,L.C., Gould,V.C., Dow,J.M., Vernikos,G.S., Okazaki,A., Sebaihia,M., Saunders,D., Arrowsmith,C., Carver,T., Peters,N., Adlem,E., Kerhornou,A., Lord,A., Murphy,L., Seeger,K., Squares,R., Rutter,S., Quail,M.A., Rajandream,M.A., Harris,D., Churcher,C., Bentley,S.D., Parkhill,J., Thomson,N.R. and Avison,M.B. (2008) Genome Biol. 9 (4), R74
2] Lucas,S., Copeland,A., Lapidus,A., Glavina del Rio,T., Dalin,E., Tice,H., Pitluck,S., Chain,P., Malfatti,S., Shin,M., Vergez,L., Lang,D., Schmutz,J., Larimer,F., Land,M., Hauser,L., Kyrpides,N., Mikhailova,N., Taghavi,S., Monchy,S., Newman,L., Vangronsveld,J., van der Lelie,D. and Richardson,P. (2008) Direct submission GenBank.
3] Crossman,L.C., Gould,V.C., Dow,J.M., Vernikos,G.S., Okazaki,A., Sebaihia,M., Saunders,D., Arrowsmith,C., Carver,T., Peters,N., Adlem,E., Kerhornou,A., Lord,A., Murphy,L., Seeger,K., Squares,R., Rutter,S., Quail,M.A., Rajandream,M.A., Harris,D., Churcher,C., Bentley,S.D., Parkhill,J., Thomson,N.R. and Avison,M.B. (2008) Genome Biol. 9 (4), R74