ISfinder

ISMsi3

Family IS3
Group IS407

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

Accession number	Transposition	Origin	Host
NC_011666	ND	Methylocella silvestris	Methylocella silvestris BL2

DNA section

IS Length : 1107 bp

Ends

IR Length : 5/7

IRL : TGACCTGCTCCCGCTAAATTAGGCCATTCTGAACTGGAATTTTCCAATTA
IRR : TGACCTCATTATAGTCTCTACGCTAAACCTCCATTTTCTCCCGGGCGTCT

Insertion site

Left flank	Direct repeat	Right flank	DR Length
TTCAAACCGA		GGCGCTGGCC	0

DNA sequence

TGACCTGCTCCCGCTAAATTAGGCCATTCTGAACTGGAATTTTCCAATTATGATCCCCGACCGGGACCAAGGAGAATTCCATGAAGGCAAGCAAGTTCAA
GGAGGCGCAGATCGCCCTCATTTTGAAGCAGGCGGAGGACGGCGTCGCCATCGCCGAGGTCTATCGCAAGGCGGGCATTTCGGATGCGACGTTTTACAAC
TGGCGCAAGAAATACGCCGGCCTGATGCCATCCGAGATGAAGCGGCTGCGCCAGCTCGAGGAAGAAAACGCCAAGCTGAAGCGGATCGTCGCTGACCTGT
CGCTCGACAAGGCCATGCTGCAGGATGTGCTATCAAAAAAGCTGTAAGGCCTGGCCGCAAGCGGGAGCTTGTCGACGCCGTTCGATCGGATTGGAAGGTG
TCGGTCAGGCGGGCCTGTTCGGCGCTACGCGTTGGTCGGGCGCTTTACGTCTACAAGTCGAAGCGTGGCGGCCAGGCCGACCTCAAACAGCGGATCAAGG
AGATTGCCGAAACGCGTGTGCGCTACGGCTATCGGTGCATTCACGTGCTGCTGCGGCGGGAAGGCTGGGCGGTGAACGCCAAGCGGATCTATCGGCTTTA
CAAGGATCTTGGCCTGCAATTGCTGAACAAGACGCCGAAGCGGCGCGTGAAGGCCAAACTGCGGGACGACCGATGCGCCGCCATGCAGCACAATGAAACC
TGGGCGATGGACTTTGTGCATGACCAACTGGCGACAGGCCGGAAGCTTCGGGTGTTGACTATAGTGGACACGTTTTCCCGGTTCTCTCCGGCTGTCGATC
CCCGCTTCTCCTATCGGGGCGAGGATGTCGTCTTGACCCTGGAGCGGATCTGCAGGAGGGTCGGCTATCCGAAGACGATCCGGGTGGATCAGGGCTCCGA
ATTCATCTCGCGCGAGACCTTGATCTGTGGGCCAATCAAAAAGGCGTCGTGCTCGACTTTTCGCGGCCTGGCAAGCCGACCGACAACGCTTTCATCGAGT
CGTTCAACGGCAAGTCCGCGCGGAATGCCTGAATGCCCATTGGTTCATGAGCCTCGAAGACGCCCGGGAGAAAATGGAGGTTTAGCGTAGAGACTATAAT
GAGGTCA

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
267 bp	88 aa	81	347	+	No

ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MKASKFKEAQIALILKQAEDGVAIAEVYRKAGISDATFYNWRKKYAGLMPSEMKRLRQLEEENAKLKRIVADLSLDKAMLQDVLSKKL

Blast result :

ORF 2

Length		Begin	End	Strand	Fusion ORF
796 bp	264 aa	296	1091	+	No

ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

PVARQGHAAGCAIKKAVRPGRKRELVDAVRSDWKMSVRRACSALRVGRALYVYKSKRGGQADLKQRIKEIAETRVRYGYRCIHVLLRREGWAVNAKRIYR
LYKDLGLQLLNKTPKRRVKAKLRDDRCAAMQHNETWAMDFVHDQLATGRKLRVLTIVDTFSRFSPAVDPRFSYRGEDVVLTLERICRRVGYPKTIRVDQG
SEFISRETLICGPIKKASCSTFRGLASRPTTLSSSRSTASPRGMPECPLVHEPRRRPGENGGLA

Blast result :

ORF 3

Length		Begin	End	Strand	Fusion ORF
1011 bp	336 aa	81	1091	+	Yes

ORF function : Transposase
Chemistry : DDE

ORF sequence :

MKASKFKEAQIALILKQAEDGVAIAEVYRKAGISDATFYNWRKKYAGLMPSEMKRLRQLEEENAKLKRIVADLSLDKAMLQDVLSKKAVRPGRKRELVDA
VRSDWKMSVRRACSALRVGRALYVYKSKRGGQADLKQRIKEIAETRVRYGYRCIHVLLRREGWAVNAKRIYRLYKDLGLQLLNKTPKRRVKAKLRDDRCA
AMQHNETWAMDFVHDQLATGRKLRVLTIVDTFSRFSPAVDPRFSYRGEDVVLTLERICRRVGYPKTIRVDQGSEFISRETLICGPIKKASCSTFRGLASR
PTTLSSSRSTASPRGMPECPLVHEPRRRPGENGGLA

Blast result :

Comments

ISMsi3 is 86 % aa similar to ISSisp1. The third ORF is a putative ORFAB transposase reconstructed in silico by possible -1 frameshift.

References

1] ISfinder annotation (2009)
2] Lucas,S., Lucas,S., Lapidus,A., Glavina del Rio,T., Dalin,E., Tice,H., Bruce,D., Goodwin,L., Pitluck,S., Forester,B., Larimer,F., Land,M., Hauser,L., Kyrpides,N., Ovchinnikova,G., Dunfield,P.F., Dedysh,S.N., Liesack,W., Stott,M.B., Smirnova,A.V., Alam,M., Chen,Y., Murrell,J.C. and Richardson,P. (2008) Direct submission GenBank.