ISStma2

  • Family IS3
  • Group IS150
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
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 flankDirect repeatRight flankDR Length
CAAGCCCCCAGGGACGGGTTCAC3
CGTGAACCCGTCCATGGGGGCTT3
GTAAACCCGTCCCTGGGGGCTTG3
GTAAACCCGTCCCTGGGGGCTTG3
GTGAACCCGTCCATGGGGGCTTG3
GTAAACCCGTCCTTGGGGGCTTG3
GTAAACCCATCCCTGGGGGCTCG3

DNA sequence

TGAAGTGACCCCCGGGAATTGGACACCAGATCCAACCCCGAGGGATACATGAACAGATACGACGCGCGTTTCAAACTGCAGGTCGCCAAAGAGGCCTGCA
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
LengthBeginEndStrandFusion ORF
522 bp173 aa49570+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MNRYDARFKLQVAKEACKTSTSVKAIARRHGLEFSTVRRWVATYRLHGWRGFHRQARFYDLPFKLAVLEKMSQDGMSGREATTYFQIGDAGAVGRWRRLY
AQGGAQALAPPPPPPRKPMKKTRSSKPPEDMSRDELLKEVAYLRAETDYLKKLDALIREEQAAQDAKRKPSKD

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
948 bp315 aa4531400+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

AAQGSRLSACGDRLPKKTRCLDPGRAGGAGRKAQAVQGLRQVHTLSLLLEAAELSRSTFYYQNHVLAHPDQDEAQLCERIRAIYDQSQGRYGYRTVTLEL
ANQGHRTNHKRVQRLMGEMGLKSRVRVKRYQAFKGAANVVVGNDLNRQFHAERPNQKWVTDVTEFKVQGMKLYLSPIMDLYNGEIVAYQIKRRPVFDLVG
QMLEEAIKKLPPDERPMIHSDQGWQYQHENYRHMLEKHSLKQSMSRRGNCLDNAAMESFFGTLKSEFFYLNSFDSIESLEAGLVEYIQYYNEERIKLKLK
GLSPIKYREQAQSAA

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
1352 bp450 aa491400+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MNRYDARFKLQVAKEACKTSTSVKAIARRHGLEFSTVRRWVATYRLHGWRGFHRQARFYDLPFKLAVLEKMSQDGMSGREATTYFQIGDAGAVGRWRRLY
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.
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