ISMca3
- Family IS3
- Group IS51
Isoform Synonym(s)
| Accession number | Transposition | Origin | Host |
|---|---|---|---|
| NC_002977 | ND | Methylococcus capsulatus | Methylococcus capsulatus Bath |
DNA section
IS Length : 1322 bp
Ends
IR Length : 16
IRL : TGAATCGCCCCGGGTTTTTGAGGAGGCTTTGACTCTTGAGAGAATTGAAG
IRR : TGAATCGCCCCGGGTTCTGTGGAGGCTGTATGGTTTGAGTTAAGTGGTTT
Insertion site
| Left flank | Direct repeat | Right flank | DR Length |
|---|---|---|---|
| CGCAGCGTCGAAGTCTGCAGC | GGTAGCCTCGTGCACCAAAGT | 0 | |
| ACAACCAGCAGACCTGGAACC | GGGGCACAAGGGGACTGGGTA | 0 |
DNA sequence
TGAATCGCCCCGGGTTTTTGAGGAGGCTTTGACTCTTGAGAGAATTGAAGCCATGAGCAAAGCCAACAAGTATTCCCCCGAAGTCCGTGAACGTGCCATC
CGCATGGTGCAGGAGCACCGTGGCGAGTATCCCTCGCTGTGGGCGGCCATCGAGTCCATTGCCCCGAAGATCGGCTGTTCGGCCAACACCCTGCATACCT
GGGTACGCACGCATGAGATCGATGCCGGTCTGCGCGCTGGCGTGACGACCGACGAACGCGAACGCCTCGAGGCCCTGGAGCGCGAGGTCAAGGAGCTGCG
CAAGGCCAACGAGATACTGAAGCTGGCGAGCGCGTTTTTCGCCCAGGCGGAGCTCGACCGCCGGCTCGAGTCCTGACTGACTTCATCGACCGGCACCGGG
ATAGCCACGGGGTCGAGCCGATCTGCAAGGTCTTGCGGATTGCCCCGTCCGGGTATTGGCGCCATGCGGCGCAGCAGCGCGACCCCCGCCTGCTTCCCGC
GCGTGCCCAGCGCGATGCGGTTCTGATGCCAGAAATTCAGCGGGTCTGGCACGCCAACATGCAGGTGTATGGCGCCGACAAGGTCTGGCGCCCGTTGAAC
CGCGAAGGTATCCAGGTCGCCCGTTGCACGGTCGAGCGCCTGATGAAGCGGTTGGGGCTGGCCGGTGTGCGGCGTGGCAAGGTGGTGCGCACCACGGTGC
CCGACCACGCCGTCCCGTGCCCGCTGGATCGGGTCAACTGGCAATTCAAGGTGGATCGTCCCAATCAGCTGTGGGTGTCGGACTTCACCTACGTCTCGAC
CTGGCAGGGCTGGTTGTATGTGGCCTTCGTGATTGACGTGTTTGCCCGGCGCATTGTGGGCTGGCGGGTCAGTCATTCGATGCGGACCGACTTCGTCCTG
GACGCACTGGAGCAGGCCCTGTACGCCCGGCAACCGGAACGCACCGATGCCCTGGTTCACCACAGCGACCGAGGCTCGCAGTACGTCTCCATCCGCTATG
CCGAGCGCCTGGCCGAGGCCGGGATCGAGCCCTCCGTCGGAAGCCGTGGCGACAGCTATGACAACGCCCTGGCCGAAACCATCAACGGCTTGTACAAGAC
CGAGCCGATCCACCGCCGAGCACCCTGGAAGAGCCGGGAGGCCGTCGAACTCGCCACCTTGGAATGGGTAGCCTGGTTCAACAACCACCGCCTGCTGGAA
TCCATCGGCTATGTCCCTCCGGTCGGGGCTGAGGCAAACTACTATCGTCGGCTCGTCGACAGAACCGTGGAAACCACTTAACTCAAACCATACAGCCTCC
ACAGAACCCGGGGCGATTCA
CGCATGGTGCAGGAGCACCGTGGCGAGTATCCCTCGCTGTGGGCGGCCATCGAGTCCATTGCCCCGAAGATCGGCTGTTCGGCCAACACCCTGCATACCT
GGGTACGCACGCATGAGATCGATGCCGGTCTGCGCGCTGGCGTGACGACCGACGAACGCGAACGCCTCGAGGCCCTGGAGCGCGAGGTCAAGGAGCTGCG
CAAGGCCAACGAGATACTGAAGCTGGCGAGCGCGTTTTTCGCCCAGGCGGAGCTCGACCGCCGGCTCGAGTCCTGACTGACTTCATCGACCGGCACCGGG
ATAGCCACGGGGTCGAGCCGATCTGCAAGGTCTTGCGGATTGCCCCGTCCGGGTATTGGCGCCATGCGGCGCAGCAGCGCGACCCCCGCCTGCTTCCCGC
GCGTGCCCAGCGCGATGCGGTTCTGATGCCAGAAATTCAGCGGGTCTGGCACGCCAACATGCAGGTGTATGGCGCCGACAAGGTCTGGCGCCCGTTGAAC
CGCGAAGGTATCCAGGTCGCCCGTTGCACGGTCGAGCGCCTGATGAAGCGGTTGGGGCTGGCCGGTGTGCGGCGTGGCAAGGTGGTGCGCACCACGGTGC
CCGACCACGCCGTCCCGTGCCCGCTGGATCGGGTCAACTGGCAATTCAAGGTGGATCGTCCCAATCAGCTGTGGGTGTCGGACTTCACCTACGTCTCGAC
CTGGCAGGGCTGGTTGTATGTGGCCTTCGTGATTGACGTGTTTGCCCGGCGCATTGTGGGCTGGCGGGTCAGTCATTCGATGCGGACCGACTTCGTCCTG
GACGCACTGGAGCAGGCCCTGTACGCCCGGCAACCGGAACGCACCGATGCCCTGGTTCACCACAGCGACCGAGGCTCGCAGTACGTCTCCATCCGCTATG
CCGAGCGCCTGGCCGAGGCCGGGATCGAGCCCTCCGTCGGAAGCCGTGGCGACAGCTATGACAACGCCCTGGCCGAAACCATCAACGGCTTGTACAAGAC
CGAGCCGATCCACCGCCGAGCACCCTGGAAGAGCCGGGAGGCCGTCGAACTCGCCACCTTGGAATGGGTAGCCTGGTTCAACAACCACCGCCTGCTGGAA
TCCATCGGCTATGTCCCTCCGGTCGGGGCTGAGGCAAACTACTATCGTCGGCTCGTCGACAGAACCGTGGAAACCACTTAACTCAAACCATACAGCCTCC
ACAGAACCCGGGGCGATTCA
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 | |
|---|---|---|---|---|---|
| 324 bp | 107 aa | 53 | 376 | + | No |
Description : First part of the transposase
ORF sequence :
MSKANKYSPEVRERAIRMVQEHRGEYPSLWAAIESIAPKIGCSANTLHTWVRTHEIDAGLRAGVTTDERERLEALEREVKELRKANEILKLASAFFAQAE
LDRRLES
LDRRLES
Blast result :ORF 2
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 849 bp | 282 aa | 433 | 1281 | + | No |
Description : Second part of the transposase
ORF sequence :
MRIAPSGYWRHAAQQRDPRLLPARAQRDAVLMPEIQRVWHANMQVYGADKVWRPLNREGIQVARCTVERLMKRLGLAGVRRGKVVRTTVPDHAVPCPLDR
VNWQFKVDRPNQLWVSDFTYVSTWQGWLYVAFVIDVFARRIVGWRVSHSMRTDFVLDALEQALYARQPERTDALVHHSDRGSQYVSIRYAERLAEAGIEP
SVGSRGDSYDNALAETINGLYKTEPIHRRAPWKSREAVELATLEWVAWFNNHRLLESIGYVPPVGAEANYYRRLVDRTVETT
VNWQFKVDRPNQLWVSDFTYVSTWQGWLYVAFVIDVFARRIVGWRVSHSMRTDFVLDALEQALYARQPERTDALVHHSDRGSQYVSIRYAERLAEAGIEP
SVGSRGDSYDNALAETINGLYKTEPIHRRAPWKSREAVELATLEWVAWFNNHRLLESIGYVPPVGAEANYYRRLVDRTVETT
Blast result :ORF 3
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 1229 bp | 409 aa | 53 | 1281 | + | Yes |
Chemistry : DDE
ORF sequence :
MSKANKYSPEVRERAIRMVQEHRGEYPSLWAAIESIAPKIGCSANTLHTWVRTHEIDAGLRAGVTTDERERLEALEREVKELRKANEILKLASAFFRPGG
ARPPARVLTDFIDRHRDSHGVEPICKVLRIAPSGYWRHAAQQRDPRLLPARAQRDAVLMPEIQRVWHANMQVYGADKVWRPLNREGIQVARCTVERLMKR
LGLAGVRRGKVVRTTVPDHAVPCPLDRVNWQFKVDRPNQLWVSDFTYVSTWQGWLYVAFVIDVFARRIVGWRVSHSMRTDFVLDALEQALYARQPERTDA
LVHHSDRGSQYVSIRYAERLAEAGIEPSVGSRGDSYDNALAETINGLYKTEPIHRRAPWKSREAVELATLEWVAWFNNHRLLESIGYVPPVGAEANYYRR
LVDRTVETT
ARPPARVLTDFIDRHRDSHGVEPICKVLRIAPSGYWRHAAQQRDPRLLPARAQRDAVLMPEIQRVWHANMQVYGADKVWRPLNREGIQVARCTVERLMKR
LGLAGVRRGKVVRTTVPDHAVPCPLDRVNWQFKVDRPNQLWVSDFTYVSTWQGWLYVAFVIDVFARRIVGWRVSHSMRTDFVLDALEQALYARQPERTDA
LVHHSDRGSQYVSIRYAERLAEAGIEPSVGSRGDSYDNALAETINGLYKTEPIHRRAPWKSREAVELATLEWVAWFNNHRLLESIGYVPPVGAEANYYRR
LVDRTVETT
Blast result :
Comments
There are 2 copies of ISMca3 in this strain. ISMca3 is 82% (ORFA) and 75% (ORFB) aa similar to ISRtr2. The third ORF is a putative ORFAB transposase reconstructed in silico by possible -1 frameshift.
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.