ISfinder Mirror Site

ISMsi4

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 : 1332 bp

Ends

IR Length : 18/26

IRL : TGGTCTGCGCCCCTTGAAGTGATCCATCCCGTATGTTGGTCCGCGGACCC
IRR : TGGCCTGTCCCCGAGGGGTGATCCAGTTTCAATGTTAGTGCATGGCGGGC

Insertion site

Left flank	Direct repeat	Right flank	DR Length
ATGCCCTCAT		GAGCGATCAA	0

DNA sequence

TGGTCTGCGCCCCTTGAAGTGATCCATCCCGTATGTTGGTCCGCGGACCCTTTGGAGGGATGGAGCGATGGGAATAAAGCGGCACAAGCCGGAGGAGATC
GTCGCCAAGCTGCGTCAGGTTGATGTCCTGACGGCGCAAGGCAAGTCGATTGCCGATGCGGTGAAAACGATCGCTGTGACGGAGGCGACGTACTTCCGCT
GGCGCGCGGAGTATGGCGGCCTGAAGAGCGGCCAGGTCAAGCGGCTGAAGGATCTGGAGCTGGAGAACGCCCGGCTGCGGCGGGCGGCGTCGGACCTGAC
CCTGGACAAGCTGATTTTGACCGAAGCCACGCGGGGACACTTCTAAGCCCCGCCCGTCGCCGCGCCTGCGTGGACAAGGTCAAAGCCGAGCTGAGAGTGT
CGGAGCGTCGCGCCTGCGCGGCGCTCCGGCAGCCCCGCTCCACACAGCGCAAGCCAGCCCGCGGCCGCGATGACGAGGCGGCTCTGACCGCCGACATCGT
CGAGCTGGCCAAGGCTTATGGCCGCTACGGCTATCGGCGGATCACGGCTTTGCTGCGCCATGCTGGCTGGGTCGTGAACGCCAAGCGGGTGCAGCGGATC
TGGCGCGCAGACAAGTTCACGCAGTCTGCGCAACAGCGCGACTGCGAGGGGCTGAAAGTCCCACAGAAACACCCAAAACGCGGCAGGCTCTGGCTGAACG
ACGGCTCTTGCGTGCGCCCGCGCGCCGAGCGGCCCAACCATGTCTGGTCCTATGACTTCGTCGCGGATCGGACCCAAGATGGACGGAAGTTCTGTATGCT
CTGTGTGATCGACGAGTTCACCCGCGAGGCCCTGGACATCCGGGTCAAACGCCGGCTCGACTCCACCGACGTGCTGGAGACCTTGGCCGATCTGATGATC
CGGCGCGGAACGCCGGCCTATGTTCGGTCGGACAATGGCCCGAGTTCATCGCCCTGGCCCGGCGCGAATGGATCGCCGCCGTCGGGTCCCAGACGGCCTA
TATCGAGCCCAGCAGCCCGTGGGAGAATGGCGCCTGCGAGAGCTTCAATTCGAAGCTCCGCGACGAGCTGCTCAATGGTGAGATGTTCTTCAGTCTGGCC
GAGGCTCAGGCGATGATCGAGGCCTGGCGGCGGCATTTCAACGCCGTGCGCCCACACAGCTCGCTCGGTTACCGATCGCCAGCGCCTGAGACAATTATTC
CCTGCGGCGGAAACATCGCGCCATGGGCGAGCGCGCCAGCTGTGGGAGCCGCGCGCTCGCCCACACCAACCATGGCGTCAGAGCCCGCCATGCACTAACA
TTGAAACTGGATCACCCCTCGGGGACAGGCCA

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
279 bp	92 aa	68	346	+	No

ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MGIKRHKPEEIVAKLRQVDVLTAQGKSIADAVKTIAVTEATYFRWRAEYGGLKSGQVKRLKDLELENARLRRAASDLTLDKLILTEATRGHF

Blast result :

ORF 2

Length		Begin	End	Strand	Fusion ORF
1175 bp	392 aa	124	1298	+	No

ORF function : Transposase
Description :

ORF sequence :

CPDGARQVDCRCGENDRCDGGDVLPLARGVWRPEERPGQAAEGSGAGERPAAAGGVGPDPGQADFDRSHAGTLLSPARRRACVDKVKAELRVSERRACAA
LRQPRSTQRKPARGRDDEAALTADIVELAKAYGRYGYRRITALLRHAGWVVNAKRVQRIWRADKFTQSAQQRDCEGLKVPQKHPKRGRLWLNDGSCVRPR
AERPNHVWSYDFVADRTQDGRKFCMLCVIDEFTREALDIRVKRRLDSTDVLETLADLMIRRGTPAYVRSDNGPPEFIALARREWIAAVGSQTAYIEPSSP
WENGACESFNSKLRDELLNGEMFFSLAEAQAMIEAWRRHFNAVRPHSSLGYRSPAPETIIPCGGNIAPWASAPAVGAARSPTPTMASEPAMH

Blast result :

ORF 3

Length		Begin	End	Strand	Fusion ORF
1231 bp	411 aa	68	1298	+	Yes

ORF function : Transposase
Chemistry : DDE

ORF sequence :

MGIKRHKPEEIVAKLRQVDVLTAQGKSIADAVKTIAVTEATYFRWRAEYGGLKSGQVKRLKDLELENARLRRAASDLTLDKLILTEATRGTLLSPARRRA
CVDKVKAELRVSERRACAALRQPRSTQRKPARGRDDEAALTADIVELAKAYGRYGYRRITALLRHAGWVVNAKRVQRIWRADKFTQSAQQRDCEGLKVPQ
KHPKRGRLWLNDGSCVRPRAERPNHVWSYDFVADRTQDGRKFCMLCVIDEFTREALDIRVKRRLDSTDVLETLADLMIRRGTPAYVRSDNGPPEFIALAR
REWIAAVGSQTAYIEPSSPWENGACESFNSKLRDELLNGEMFFSLAEAQAMIEAWRRHFNAVRPHSSLGYRSPAPETIIPCGGNIAPWASAPAVGAARSP
TPTMASEPAMH

Blast result :

Comments

ISMsi4 is 75% aa similar to ISMex5. The third oRF is a putative ORFAB reconstructed in silico by possible -1 frameshift.
The ORFB is also reconstructed in silico by joining (124-942;939-1298).

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.