ISfinder

ISMch2

Family IS5
Group IS427

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

Accession number	Transposition	Origin	Host
NC_011758	ND	Methylobacterium chloromethanicum	Methylobacterium chloromethanicum CM4 plasmid pMCHL01

DNA section

IS Length : 861 bp

Ends

IR Length : 15/16

IRL : GAGTGCCTAACAGAACGGCACGAAGCGGTCGGATCGGCGTTGGTTGGGTA
IRR : GAGCGCCTAACAGAACCGTTTGATCTGGTTGAGGGTAATGAGACTTGCCG

Insertion site

Left flank	Direct repeat	Right flank	DR Length
GGAACCTCGTAGGC	TTA	GACCCTGCAATG	3
GCAGTGGCACGTAA		TTAATCGCTT	0

DNA sequence

GAGTGCCTAACAGAACGGCACGAAGCGGTCGGATCGGCGTTGGTTGGGTATGGCTCGCCCTCTGCTTCCCGACGATCTCTGGACCGAGATCGCCCCGCTC
CTGCCGCCGCCTCGGCCGCGCCCGAAGGGCGGACGGCCTCCCATCGATAATCGGGCAGCGCTGACCGGCATCGTGTTCGTGCTACGCTCCGGCCTGCCTT
GGGAGATGCTGCCGGCGGAGATGGGCTGCGGCTGCGGGATGAGTTGCTGGCGGCGTCTGCGCGACTGGCAGGTGGCCGGTGTGTGGGCACGGCTGCATCA
GGTTCTCTTGGAGCGTCTGCACGCGGCCGGTGAGATCGATTGGCGTCGGGCGAGCTTGGACCGTGCCTCTGTCCCAGCCAAAAAGGGGGGCCTGCCACGG
GCCCGAACCCGACGGACCGGGCCAAGCCGGGCACGAAACGCCACATCGTCACCGACGCCCGCGGTACGCCGCTCGGCTTGAGACTGACCGAGGCCAACCG
ACACGACAGCCCGCAGATGGCGCCGACCCTCGATGCCATCCCGCCACTGAGCACGGGCCGGCGTGGTCGACCGCGCCGACGCCCCGACAAGCTGCACGCC
GACAAGGCCTATGACGCCAAGGCACGCCGACAGGAGTGTCGAGCCCGCGGCATCGTCCCACGCATCGCCCGCAAGGGCATCGAAAGCAGCGAGAAGCTCG
GTCGACACCGCTGGGTGGTTGAGCGCACTCACGCTTGGTTCAACCGCTTCCGCCGCCTGCCGATCCGCTACGAGCGACGCGCCGACATCTACGAGGCCTT
CACCAGACTCGCGGCAAGTCTCATTACCCTCAACCAGATCAAACGGTTCTGTTAGGCGCTC

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
432 bp	143 aa	50	481	+	No

ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MARPLLPDDLWTEIAPLLPPPRPRPKGGRPPIDNRAALTGIVFVLRSGLPWEMLPAEMGCGCGMSCWRRLRDWQVAGVWARLHQVLLERLHAAGEIDWRR
ASLDRASVPAKKGGLPRARTRRTGPSRARNATSSPTPAVRRSA

Blast result :

ORF 2

Length		Begin	End	Strand	Fusion ORF
522 bp	173 aa	334	855	+	No

ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

DRLASGELGPCLCPSQKGGPATGPNPTDRAKPGTKRHIVTDARGTPLGLRLTEANRHDSPQMAPTLDAIPPLSTGRRGRPRRRPDKLHADKAYDAKARRQ
ECRARGIVPRIARKGIESSEKLGRHRWVVERTHAWFNRFRRLPIRYERRADIYEAFTRLAASLITLNQIKRFC

Blast result :

ORF 3

Length		Begin	End	Strand	Fusion ORF
806 bp	268 aa	50	855	+	Yes

ORF function : Transposase
Chemistry : DDE

ORF sequence :

MARPLLPDDLWTEIAPLLPPPRPRPKGGRPPIDNRAALTGIVFVLRSGLPWEMLPAEMGCGCGMSCWRRLRDWQVAGVWARLHQVLLERLHAAGEIDWRR
ASLDRASVPAKKGGPATGPNPTDRAKPGTKRHIVTDARGTPLGLRLTEANRHDSPQMAPTLDAIPPLSTGRRGRPRRRPDKLHADKAYDAKARRQECRAR
GIVPRIARKGIESSEKLGRHRWVVERTHAWFNRFRRLPIRYERRADIYEAFTRLAASLITLNQIKRFC

Blast result :

Comments

ISMch2 is 74% aa similar to ISBcen20. The third ORF is a putative ORFAB transposase reconstructed in silico by possible -1 frameshift.

References

1] ISfinder annotation (2009)
2] Lucas,S., Copeland,A., Lapidus,A., Glavina del Rio,T., Dalin,E., Tice,H., Bruce,D., Goodwin,L., Pitluck,S., Chertkov,O., Brettin,T., Detter,J.C., Han,C., Larimer,F., Land,M., Hauser,L., Kyrpides,N., Mikhailova,N., Marx,C. and Richardson,P. (2008) Direct submission GenBank.