ISfinder Mirror Site

ISMca6

Family ISAs1
Group

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

Accession number	Transposition	Origin	Host
NC_002977	ND	Methylococcus capsulatus	Methylococcus capsulatus Bath

DNA section

IS Length : 1180 bp

Ends

IR Length : 17/21

IRL : CAGGGCTGTTCAATGCTGAAAAATTGATGTAAGAAGTCAAGATTTTCAAA
IRR : CAGGGTTGTTCAACGCTAAATACCGTCATAGGCCAAGAGCCGGTGGAGGC

Insertion site

Left flank	Direct repeat	Right flank	DR Length
AGATCAGCCG	GTTGTCGAAG	GTGGCTCAGG	10
CTTCTCCCAG	AGGGAGAGGG	TATGTTGTCC	10

DNA sequence

CAGGGCTGTTCAATGCTGAAAAATTGATGTAAGAAGTCAAGATTTTCAAAGAGGTTCCCGTTGTCCGCCCTGAAACAAAGCCTGCTGGCCATTCCGGATC
ATCGCCGTGCCCAGGGGCGGCTGTTCGACCTGCCCCATATGCTGCTGTTCAGCATCTTGGCGATCATGAGCGGCGCGACGTCCTACCGGCGCATTCATCA
GTTCCTGCACACCCATCAGGCGGCATTGAACGCGGCCTTCGGTTGCCGGTGGCGCCGCACGCCGGCTTACAGTTCGATCCGCTATGCCTTGCAGGGCTTG
GACGTGCAAGCCCTGGCGCCGCATTTTCGCGCCCATGCCGCGCGCTTGGCCGAAGGGGCGGCGGTGATCGCGCTCGACGGCAAGACCTTGCGCGGCAGCC
TGGACCGTTTCGAGGACCGCAAGGCCGCCCAGGTGCTCAGCGCCTTCGCCACCGAAGAGCGGATCGTGCTGGGCCAGATCCTGATCGAGGATGCGGGCAA
GGACCATGAAATCCAGGCGGCCCAGCGCCTCATCGAAACCTTGGGGCTGAGCGGACGGCTCTATACGCTCGATGCCCTCCACCTTCAAAAAAACGGTTGA
AACCGTGCTTGCCACCGGCAACGACCTCCTGGTGCAGCTCAAAGGCAATCATCCCAAGCTGCTGGCCGCGGTGCGAACGCTGTGCCAGAGCCGAGCCCAC
GCTGAACAGAGCTACACCGTCGACCTGGGCCGGCGCAACCGCATCGAACAGCGCACCGTGCGCCTGTGGCCGCTCCCGCCGGGCAGCGGCACCGACCCCT
GGCATGACCACTTCCAGACCGTGATCGAGGGGCAGCGCCAGATCGAAGTTTTCAATCCCTACCACCGCCGCTTCGAGCCCCGCCAGGAATCCCCTGCTTA
TTACTTGGCGACCTGCACCGCCTCGGCGGCCACTTTAGCTCAGGTCATCCGCGGCCATTGGGCCATCGAAAACCGCCTTCATCATGTGCTCGATGTCTCC
CTCGGCGAGGACTCCAGCCGCATCCGCCGAAATCCCGGCGTCTTTGCCCTGCTGCGCCACTTCGCCTTGAACCTCTTGCGACATAATGGACAAGCCAACA
TCCGCTCCGCCCTTTACGACAACGCCATCTGCCTCCACCGGCTCTTGGCCTATGACGGTATTTAGCGTTGAACAACCCTG

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
540 bp	179 aa	61	600	+	No

ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MSALKQSLLAIPDHRRAQGRLFDLPHMLLFSILAIMSGATSYRRIHQFLHTHQAALNAAFGCRWRRTPAYSSIRYALQGLDVQALAPHFRAHAARLAEGA
AVIALDGKTLRGSLDRFEDRKAAQVLSAFATEERIVLGQILIEDAGKDHEIQAAQRLIETLGLSGRLYTLDALHLQKNG

Blast result :

ORF 2

Length		Begin	End	Strand	Fusion ORF
594 bp	197 aa	572	1165	+	No

ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

MPSTFKKTVETVLATGNDLLVQLKGNHPKLLAAVRTLCQSRAHAEQSYTVDLGRRNRIEQRTVRLWPLPPGSGTDPWHDHFQTVIEGQRQIEVFNPYHRR
FEPRQESPAYYLATCTASAATLAQVIRGHWAIENRLHHVLDVSLGEDSSRIRRNPGVFALLRHFALNLLRHNGQANIRSALYDNAICLHRLLAYDGI

Blast result :

ORF 3

Length		Begin	End	Strand	Fusion ORF
1105 bp	0 aa	61	1165	-	Yes

ORF function : Transposase
Chemistry : Unknow

ORF sequence :

Blast result :

Comments

There are 2 or more copies of ISMca6 in this strain. ISMca6 is 48% aa similar to ISEc5.

References

1] Ward,N., Larsen,O., Sakwa,J., Bruseth,L., Khouri,H., Durkin,A.S., Dimitrov,G., Jiang,L., Scanlan,D., Kang,K.H., Lewis,M., Nelson,K.E., Methe,B., Wu,M., Heidelberg,J.F., Paulsen,I.T., Fouts,D., Ravel,J., Tettelin,H., Ren,Q., Read,T., DeBoy,R.T., Seshadri,R., Salzberg,S.L., Jensen,H.B., Birkeland,N.K., Nelson,W.C., Dodson,R.J., Grindhaug,S.H., Holt,I., Eidhammer,I., Jonasen,I., Vanaken,S., Utterback,T., Feldblyum,T.V., Fraser,C.M., Lillehaug,J.R. and Eisen,J.A. (2004) PLoS Biol. 2(10):e303.