ISMca4
- Family IS3
- Group IS407
Isoform Synonym(s)
| Accession number | Transposition | Origin | Host |
|---|---|---|---|
| NC_002977 | ND | Methylococcus capsulatus | Methylococcus capsulatus Bath |
DNA section
IS Length : 1197 bp
Ends
IR Length : 13/17
IRL : TGGGGCAATCCCCCCGGCCAATGAAGGGGTTCAGAAGTAGAATTTTCTCG
IRR : TCCGGTAATCCTCCCGGAATTAGGGGAGATCAGAAGTAGAGCTATGCGGC
Insertion site
| Left flank | Direct repeat | Right flank | DR Length |
|---|---|---|---|
| AGGGCGAAACCTTTTGC | TGGGCGCAGGCCGACAG | 0 |
DNA sequence
TGGGGCAATCCCCCCGGCCAATGAAGGGGTTCAGAAGTAGAATTTTCTCGTTAATGGGGAGTTCTGCATGAAGAAGTCGAAGTTTTCGGACAGCCAGATC
ATCGAGGCGCTGAAGCGGGTTGAAGCCGGGCTGTCGGTGCCAAAGTTGTGCCGGGAATTGGGGATCAGCACGGCGGCGTTTTGCAAGTGGCGAGCGAAGC
ATGGCGGCCTGGCCGTGTCGATGATGGCCCGGATGAAGGAACTGGAAGCCGAGAATGCCCGGCTGAATGAAGATGCACGCGGAGGAGCGCCTGAAGGCCG
ACATTCTTCAGGAGGCGATTTCAAAAAAGTGGTGAGGCCATCTCACCTCCGCGCGACGGCCAGGCGTGCTGTCAGCGGGCACAGGGTGTCAATCCGCCTT
GGCTGCGCGGCATTTCAGGTCAGCGGAACCTGTTATCGGCACAGCGCCAAGCGCAATGCCGGGAACGAAGAAATCGCCGACTGGCTGATGCGGCTGACCG
ACAACCACCGCAACTGGGGATTCGGGCTGTGCTTCCTGTATTTGCGCAATGTGAAAGGATTTGGCTGGAACCACAAACGTGTGTGCCGGATATGCCGCGA
ACTGGAACTGAATCTTCGCATCAAGCCGAGGAAACGGCTGAAACGGGACAAGCCTGAACCGCTCACGGCGCCGACACGGATCAACCAAGTCTGGTCGATG
GACTTCATGCATGATCAGCGCGCAGATGGAAGGAAGTTCAGGTTGTTCAATGTGATTGATGACTTCAACCGCGCGTCGCTAGGGATGGAGGTGGACTTCT
CGCCGCCGTCCGAGCGCGTCACCCGCGCCCTGGAGCAAGTGATGGAATGGCGGGGGCGACCACGGGTGATCCGCTGCGACAACGGGCCGGAGAATATCAG
CGCGAAGGTCCAGGCCAGGGCGGCACGGCAAGGCATCCGGATTGAATGCATCCAGCCGGGCAACCCGCAGCAGAACGCGCATGTGGAGCGATTCAACCGC
ACGGTGCGCCATGAATGGCTGTCGCAGTATGACTGGGAGTCACTGGATGAAGTGCAGGCATTCGCAACACGCTGGATGTGGACGTACAATCACGAACGCC
CAAACATGGCCTTGGGCGGCATCACGCCAAAACAGCGGTTGGCCAGGGCCGCATAGCTCTACTTCTGATCTCCCCTAATTCCGGGAGGATTACCGGA
ATCGAGGCGCTGAAGCGGGTTGAAGCCGGGCTGTCGGTGCCAAAGTTGTGCCGGGAATTGGGGATCAGCACGGCGGCGTTTTGCAAGTGGCGAGCGAAGC
ATGGCGGCCTGGCCGTGTCGATGATGGCCCGGATGAAGGAACTGGAAGCCGAGAATGCCCGGCTGAATGAAGATGCACGCGGAGGAGCGCCTGAAGGCCG
ACATTCTTCAGGAGGCGATTTCAAAAAAGTGGTGAGGCCATCTCACCTCCGCGCGACGGCCAGGCGTGCTGTCAGCGGGCACAGGGTGTCAATCCGCCTT
GGCTGCGCGGCATTTCAGGTCAGCGGAACCTGTTATCGGCACAGCGCCAAGCGCAATGCCGGGAACGAAGAAATCGCCGACTGGCTGATGCGGCTGACCG
ACAACCACCGCAACTGGGGATTCGGGCTGTGCTTCCTGTATTTGCGCAATGTGAAAGGATTTGGCTGGAACCACAAACGTGTGTGCCGGATATGCCGCGA
ACTGGAACTGAATCTTCGCATCAAGCCGAGGAAACGGCTGAAACGGGACAAGCCTGAACCGCTCACGGCGCCGACACGGATCAACCAAGTCTGGTCGATG
GACTTCATGCATGATCAGCGCGCAGATGGAAGGAAGTTCAGGTTGTTCAATGTGATTGATGACTTCAACCGCGCGTCGCTAGGGATGGAGGTGGACTTCT
CGCCGCCGTCCGAGCGCGTCACCCGCGCCCTGGAGCAAGTGATGGAATGGCGGGGGCGACCACGGGTGATCCGCTGCGACAACGGGCCGGAGAATATCAG
CGCGAAGGTCCAGGCCAGGGCGGCACGGCAAGGCATCCGGATTGAATGCATCCAGCCGGGCAACCCGCAGCAGAACGCGCATGTGGAGCGATTCAACCGC
ACGGTGCGCCATGAATGGCTGTCGCAGTATGACTGGGAGTCACTGGATGAAGTGCAGGCATTCGCAACACGCTGGATGTGGACGTACAATCACGAACGCC
CAAACATGGCCTTGGGCGGCATCACGCCAAAACAGCGGTTGGCCAGGGCCGCATAGCTCTACTTCTGATCTCCCCTAATTCCGGGAGGATTACCGGA
Protein section
ORF number : 1
ORF 1
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 1089 bp | 362 aa | 68 | 1156 | + | No |
Chemistry : DDE
ORF sequence :
MKKSKFSDSQIIEALKRVEAGLSVPKLCRELGISTAAFYKWRAKHGGLAVSMMARMKELEAENARLNEDARGGAPEGRHSSGGDFKKVVRPSHLRATARR
AVSGHRVSIRLGCAAFQVSGTCYRHSAKRNAGNEEIADWLMRLTDNHRNWGFGLCFLYLRNVKGFGWNHKRVCRICRELELNLRIKPRKRLKRDKPEPLT
APTRINQVWSMDFMHDQRADGRKFRLFNVIDDFNRASLGMEVDFSPPSERVTRALEQVMEWRGRPRVIRCDNGPENISAKVQARAARQGIRIECIQPGNP
QQNAHVERFNRTVRHEWLSQYDWESLDEVQAFATRWMWTYNHERPNMALGGITPKQRLARAA
AVSGHRVSIRLGCAAFQVSGTCYRHSAKRNAGNEEIADWLMRLTDNHRNWGFGLCFLYLRNVKGFGWNHKRVCRICRELELNLRIKPRKRLKRDKPEPLT
APTRINQVWSMDFMHDQRADGRKFRLFNVIDDFNRASLGMEVDFSPPSERVTRALEQVMEWRGRPRVIRCDNGPENISAKVQARAARQGIRIECIQPGNP
QQNAHVERFNRTVRHEWLSQYDWESLDEVQAFATRWMWTYNHERPNMALGGITPKQRLARAA
Blast result :
Comments
There are 3 copies of ISMca4 in this strain. ISMca4 is 76% aa similar to ISXcd1. There is no programmed -1 frameshift.
For the ends of this element there are two possibilities :
* with IRL : TGGGGCAA and IRR : TCCGGTAA, according to the concensus of the IS3 family
* with IRL : GGCAA and IRR : GGTAA (3 nucleotides are missing in two copies).
For the ends of this element there are two possibilities :
* with IRL : TGGGGCAA and IRR : TCCGGTAA, according to the concensus of the IS3 family
* with IRL : GGCAA and IRR : GGTAA (3 nucleotides are missing in two copies).
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.