ISfinder Mirror Site

ISStma13

Family IS3
Group IS407

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 : 1216 bp

Ends

IR Length : 35/50

IRL : TGCGACGTCCCCCCGAGATTGAGTAGCGAAGCGGTTTGGAGTCCAATCCT
IRR : TGCGCACGCGACGTCCCCCCGGCTTGAGTAGTGGGCGGGTTTAGAGTCCG

Insertion site

Left flank	Direct repeat	Right flank	DR Length
ATGCCAAACG		ATTACATGGG	0

DNA sequence

TGCGACGTCCCCCCGAGATTGAGTAGCGAAGCGGTTTGGAGTCCAATCCTCAATGACAAGGAGATTGGACGTGAAGAAGCGCTTTTCCGAAGAGCAGATC
ATCGGCTTCCTACGCGAAGCTGAGTCCGGCATGCCCATCAAGGACCTCTGCCGCCAGCATGGCTTCAGCGAGGCCTCGTACTACCTGTGGCGCAGCAAGT
TCGGCGGCATGAGCGTGCCCGACGCCAAGCGGCACAAGGATCTGGAGGCGGAGAACACACGCCTGAAGAAGCTGCTGGCAGAACAGGTCTTCGAGAACGA
CGTCATCAAGGATGCGTTGCGAAAAAAGTGGTGACCGCGCCGGCGCGCAGGCTGCTGGTGCGGAGCATGGTCGAGAAGGGGTTGAGCGAGCGGCGAGCGC
TGACGGTGGTGCGGATGAGCGCTAGCGCGCTGCGCTATGAGCCTCGGCCCGACAACAACGTTGAGCTGCGCGAGCAGATTGCTGCGCTGGCGCATCGGCA
CAGACGCTACGGGGTGGGCATGATCCATCTGAAGCTGCGGCAGAAAGGACTTGTCGTGAACTACAAGCGAGTGGAGCGGCTCTATCAGGAAGCGGGCCTG
CAGGTGCGACGCAGAAAGCGTAAGAAGGTGCCGGTTAGCGAGCGCCAGCCCCTCCTGCGGCCGTCCGCTGCCAATGAGGTGTGGTCGATGGACTTCGTGT
TCGAGCGTACCGCAGAAGGCCGGGTGGTCAAGTGCCTGACGATCGTCGACGACGCCACCCACGAGGCTGTGGCCATCGAAGTGGAGCGGGCAATATCCGG
GCAAGGCGTGTCCAGGGTACTGGACAGGCTGGCCATGCAGCGCGGCTTGCCACGAGTGATCAGGACAGACAACGGCAAGGAGTTTTGCGGTAAGGCGATG
GTGGCTTGGGCTCACGAAAAGGAAGTTGCCCTGCGTCTGATCGAACCGGGCAAGCCGAACCAAAATGCGTACATCGAGTCCTTCAACGGACGGCTGCGCG
ACGAATGCCTCAACGAGCACTGGTTCCCGACGTTGCTTCATGCCCGCACCAGTATCGAAAGCTGGCGGCGCGACTACAACGAAGAAAGACCAAAAAGAGC
GCTTGGCGGTCTAACACCCGCCCAATACGCCGCGCAGTTGGCGGCGAAGAACGATAACATCAGCACCGGACTCTAAACCCGCCCACTACTCAAGCCGGGG
GGACGTCGCGTGCGCA

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
282 bp	93 aa	53	334	+	No

ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MTRRLDVKKRFSEEQIIGFLREAESGMPIKDLCRQHGFSEASYYLWRSKFGGMSVPDAKRHKDLEAENTRLKKLLAEQVFENDVIKDALRKKW

Blast result :

ORF 2

Length		Begin	End	Strand	Fusion ORF
1053 bp	350 aa	124	1176	+	No

ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

VRHAHQGPLPPAWLQRGLVLPVAQQVRRHERARRQAAQGSGGGEHTPEEAAGRTGLRERRHQGCVAKKVVTAPARRLLVRSMVEKGLSERRALTVVRMSA
SALRYEPRPDNNVELREQIAALAHRHRRYGVGMIHLKLRQKGLVVNYKRVERLYQEAGLQVRRRKRKKVPVSERQPLLRPSAANEVWSMDFVFERTAEGR
VVKCLTIVDDATHEAVAIEVERAISGQGVSRVLDRLAMQRGLPRVIRTDNGKEFCGKAMVAWAHEKEVALRLIEPGKPNQNAYIESFNGRLRDECLNEHW
FPTLLHARTSIESWRRDYNEERPKRALGGLTPAQYAAQLAAKNDNISTGL

Blast result :

ORF 3

Length		Begin	End	Strand	Fusion ORF
1124 bp	374 aa	53	1176	+	Yes

ORF function : Transposase
Chemistry : DDE

ORF sequence :

MTRRLDVKKRFSEEQIIGFLREAESGMPIKDLCRQHGFSEASYYLWRSKFGGMSVPDAKRHKDLEAENTRLKKLLAEQVFENDVIKDALRKKVVTAPARR
LLVRSMVEKGLSERRALTVVRMSASALRYEPRPDNNVELREQIAALAHRHRRYGVGMIHLKLRQKGLVVNYKRVERLYQEAGLQVRRRKRKKVPVSERQP
LLRPSAANEVWSMDFVFERTAEGRVVKCLTIVDDATHEAVAIEVERAISGQGVSRVLDRLAMQRGLPRVIRTDNGKEFCGKAMVAWAHEKEVALRLIEPG
KPNQNAYIESFNGRLRDECLNEHWFPTLLHARTSIESWRRDYNEERPKRALGGLTPAQYAAQLAAKNDNISTGL

Blast result :

Comments

ISStma13 is 89% aa similar to IS1404. 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