ISMsi4
- Family IS3
- Group IS407
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
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 |
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 |
Description :
ORF sequence :
CPDGARQVDCRCGENDRCDGGDVLPLARGVWRPEERPGQAAEGSGAGERPAAAGGVGPDPGQADFDRSHAGTLLSPARRRACVDKVKAELRVSERRACAA
LRQPRSTQRKPARGRDDEAALTADIVELAKAYGRYGYRRITALLRHAGWVVNAKRVQRIWRADKFTQSAQQRDCEGLKVPQKHPKRGRLWLNDGSCVRPR
AERPNHVWSYDFVADRTQDGRKFCMLCVIDEFTREALDIRVKRRLDSTDVLETLADLMIRRGTPAYVRSDNGPPEFIALARREWIAAVGSQTAYIEPSSP
WENGACESFNSKLRDELLNGEMFFSLAEAQAMIEAWRRHFNAVRPHSSLGYRSPAPETIIPCGGNIAPWASAPAVGAARSPTPTMASEPAMH
LRQPRSTQRKPARGRDDEAALTADIVELAKAYGRYGYRRITALLRHAGWVVNAKRVQRIWRADKFTQSAQQRDCEGLKVPQKHPKRGRLWLNDGSCVRPR
AERPNHVWSYDFVADRTQDGRKFCMLCVIDEFTREALDIRVKRRLDSTDVLETLADLMIRRGTPAYVRSDNGPPEFIALARREWIAAVGSQTAYIEPSSP
WENGACESFNSKLRDELLNGEMFFSLAEAQAMIEAWRRHFNAVRPHSSLGYRSPAPETIIPCGGNIAPWASAPAVGAARSPTPTMASEPAMH
Blast result :ORF 3
Length | Begin | End | Strand | Fusion ORF | |
---|---|---|---|---|---|
1231 bp | 411 aa | 68 | 1298 | + | Yes |
Chemistry : DDE
ORF sequence :
MGIKRHKPEEIVAKLRQVDVLTAQGKSIADAVKTIAVTEATYFRWRAEYGGLKSGQVKRLKDLELENARLRRAASDLTLDKLILTEATRGTLLSPARRRA
CVDKVKAELRVSERRACAALRQPRSTQRKPARGRDDEAALTADIVELAKAYGRYGYRRITALLRHAGWVVNAKRVQRIWRADKFTQSAQQRDCEGLKVPQ
KHPKRGRLWLNDGSCVRPRAERPNHVWSYDFVADRTQDGRKFCMLCVIDEFTREALDIRVKRRLDSTDVLETLADLMIRRGTPAYVRSDNGPPEFIALAR
REWIAAVGSQTAYIEPSSPWENGACESFNSKLRDELLNGEMFFSLAEAQAMIEAWRRHFNAVRPHSSLGYRSPAPETIIPCGGNIAPWASAPAVGAARSP
TPTMASEPAMH
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).
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.
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.