ISfinder Mirror Site

ISStma5

Family IS3
Group IS3

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

Accession number	Transposition	Origin	Host
NC_010943	ND	Stenotrophomonas maltophilia	Stenotrophomonas maltophilia K279a

DNA section

IS Length : 1228 bp

Ends

IR Length : 20/26

IRL : TGGGGTTCACCCCCGTTTTCACGGACACTTACGAGAAGGCCGATCAAGGC
IRR : TCGGGTTCTACCCCGAAATCACGGACGGTTGTAAAAGGGCTGAGAACTTC

Insertion site

Left flank	Direct repeat	Right flank	DR Length
AGGATAAGGC	AT	TCAGGAGCTG	2
CGACGGCGAT	CC	AATCTCGCAC	2

DNA sequence

TGGGGTTCACCCCCGTTTTCACGGACACTTACGAGAAGGCCGATCAAGGCCATGAGGAGTGTTCATGTCGAAGCGAAGGAAGTTCAGCACCGAGTTCAAG
CGCGGTGCGGTTGAGCAGGCCAGCCAGCCGGGCGTCAGCTGTGCCCAGGTGGCCCGGGAGCTGGGGATCCGGGATGCATTGCTGACCCGCTGGAAGCGGG
AGGCCCAGAGCCGGGGCCAGGTGGCCTTCGGTGGCACCGGGACGCCCCGGGACGAGGAACTGGCGCGGCTCAAGCGCGAGCTGGCCCGGGTGAAGAAGGA
GCGGGATTTTTTGCGAGAAGCGGCGACGTTCTTTGCCAAGGGATCATCCTGAGGTATCAGGTGATCGAACGTTGCCGCGATGAGTTTCCAGTGCGACTGA
TGTGTCGTTGCCTGCGGGTCTCGGCCAGCGGTTACTACGACTGGAGTAAGCGCTTGCCCAGTGCCCGGGAGCGCGACAACCAGCGCTTGCTCGGCCGGAT
CCGTGAGTTGCATGAGGACAGCCGGGGCACATTGGGCGCCGGCCGGATGCATGAAGACCTTGCCGAGGAAGGCGAGACGGCGAGCCTGAACCGGGTGGCG
CGTCTGATGGCGACCGATGGCCTGCAGGGTTGGCCGCGACCGAAGCGGCGAGGCCAGCGCGGCAAGCCGGCGCTGACGCCGCCGGGTGTGCGCAACCTGC
TGGAGCGGGACTTCACCGCGTTGGAGCCGGAGACCAGGTGGGTCACCGACATCACCGAGCTCAAGACCCGGCAAGGCAAGCTGTATCTGTGCATCGTGCT
GGACCTGTTTGACCAGCGGGTGGTGGGGTGGTCAATGCATCATCGTCAGGATCGTCAGATGGTGATCAGGGCCGTGCAGATGGCGGTCTGGCAGCGCCAA
GGCAGCCATCCACTGATCCTGCACTCCGACCGTGGCAGCCAGTTCCGAAGCGGCGACTACCAGCGTTACCTGGCGGCCAACGGCTTGGTGTGCTCGATGA
GCGCGGTGGGCCACTGCGGTGACAACGCCGCGTGCGAAGGCTTCTTCGGCCTGCTCAAGCGCGAGCGGGTCTACCGCATGACCTACCCAACGCTCGATGC
CGCGAGGGCGGATGTGTTCGAATACATCGAGCGGTTCCACAACCCGAGGATGCGACGAAGGGTCGCCAGGCAAGACCAGAAGTTCTCAGCCCTTTTACAA
CCGTCCGTGATTTCGGGGTAGAACCCGA

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
288 bp	95 aa	65	352	+	No

ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MSKRRKFSTEFKRGAVEQASQPGVSCAQVARELGIRDALLTRWKREAQSRGQVAFGGTGTPRDEELARLKRELARVKKERDFLREAATFFAKGSS

Blast result :

ORF 2

Length		Begin	End	Strand	Fusion ORF
1107 bp	368 aa	115	1221	+	No

ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

AGQPAGRQLCPGGPGAGDPGCIADPLEAGGPEPGPGGLRWHRDAPGRGTGAAQARAGPGEEGAGFFARSGDVLCQGIILRYQVIERCRDEFPVRLMCRCL
RVSASGYYDWSKRLPSARERDNQRLLGRIRELHEDSRGTLGAGRMHEDLAEEGETASLNRVARLMATDGLQGWPRPKRRGQRGKPALTPPGVRNLLERDF
TALEPETRWVTDITELKTRQGKLYLCIVLDLFDQRVVGWSMHHRQDRQMVIRAVQMAVWQRQGSHPLILHSDRGSQFRSGDYQRYLAANGLVCSMSAVGH
CGDNAACEGFFGLLKRERVYRMTYPTLDAARADVFEYIERFHNPRMRRRVARQDQKFSALLQPSVISG

Blast result :

ORF 3

Length		Begin	End	Strand	Fusion ORF
1157 bp	385 aa	65	1221	+	Yes

ORF function : Transposase
Chemistry : DDE

ORF sequence :

MSKRRKFSTEFKRGAVEQASQPGVSCAQVARELGIRDALLTRWKREAQSRGQVAFGGTGTPRDEELARLKRELARVKKERDFFARSGDVLCQGIILRYQV
IERCRDEFPVRLMCRCLRVSASGYYDWSKRLPSARERDNQRLLGRIRELHEDSRGTLGAGRMHEDLAEEGETASLNRVARLMATDGLQGWPRPKRRGQRG
KPALTPPGVRNLLERDFTALEPETRWVTDITELKTRQGKLYLCIVLDLFDQRVVGWSMHHRQDRQMVIRAVQMAVWQRQGSHPLILHSDRGSQFRSGDYQ
RYLAANGLVCSMSAVGHCGDNAACEGFFGLLKRERVYRMTYPTLDAARADVFEYIERFHNPRMRRRVARQDQKFSALLQPSVISG

Blast result :

Comments

ISStma5 is 92% aa similar to ISXc8. The third ORF is a putative ORFAB transposase reconstructed in silico by possible -1 frameshift.

References

1] ISfinder annotation (2009)
2] 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