ISDvu3
- Family IS3
- Group IS407
Isoform Synonym(s)
Accession number | Transposition | Origin | Host |
---|---|---|---|
NC_002937 | ND | Desulfovibrio vulgaris | Desulfovibrio vulgaris subsp. vulgaris Hildenborough |
DNA section
IS Length : 1208 bp
Ends
IR Length : 16/18
IRL : TGACCTGCCCGGCACTTTTCAGACCAGCCGAAACTTGAGATAGGTTTCTC
IRR : TGACCTGCCGGGAAACTTCGGACCACTCAATTCTTGATGGTTTCCCCACG
Insertion site
Left flank | Direct repeat | Right flank | DR Length |
---|---|---|---|
GGGGTCGATA | TCTTAAGAGC | 0 |
DNA sequence
TGACCTGCCCGGCACTTTTCAGACCAGCCGAAACTTGAGATAGGTTTCTCCCTCAACCACGAGGGAACCGATGAAAAAGGGACGATTTTCCGAAGAGCAG
ATGGTCGGCATTCTGCGAGAAGCTGACCGTAGTCCAGTGGCCCAGGTGGCCAAGAAGCATGGAATCAGCGAGCAGACGATCTACACATGGCGCCAGCGGT
TCGCAGGCATGTCCGCCGATGACGTGAAGCGGCTACGCCTGCTGGAACAAGAGAACACGCGGCTGAAGAAGATACTTGCGGAACGGGACCTTGAAATCGA
GGTCATGAAGGAAATCGCCACAAAAAAATGGTAGGCGCACCCGTCCGACGCATCCAGGTGGCATACGCTAGGAGTCGCGGGCTTTCACAACGCAGGGCGT
GTGCGCTGTTATCCACTTCCCGGTCGTCGCTCCACTACGAGTCACGGCTGGAGGCTCGGGACAAGCCCCTGATGGCGGCGATGTCAGGTCTAGCTGCGGC
GTATCCGCGCTTTGGATATCGCCGGATCAACGTGTTCATGGAGCGTCTGGGTCATGTCATGGGGGCCGACAAGGCGTTCCGGCTTTGATGCAAGGCCGGG
TTGCAGGTGCCCAGAAAGCGGCCTCGGAAGCGGATTGCGGCGTCCCGTCCGCGACCACAACTGCCGATGGGTGCAAACGAACTGTGGGCGTACGACTTTG
TCTACGACGCCTGTGCAAATGGTCAGCCGATAAAATGCCTGACCGTGGTGGACGAATACACGCGCGAATGCCTGGCTATAGACGTTGCCGGGAGCATCAG
GTCGGGCCGGGTGATTGAGGTGCTGTCCCGCCTGATTAGTGAACGTGGAGCCCCTCTGAGCCTACGTTCTGACAACGGACCGGAGTTCGTGTCGAAGGCA
CTGCTCAGATGGGCGGCTCGGGAGTCTCTGAATCTGGCTCTGATTGAGCCTGGCAAGCCCTGGCAGAACGGTTTGAACGAGAGTTTTAATGGCAAATTTC
GCGACGAATGTCTGTCAATGGAATGGTTCCGGTGTCGGGACGAGGCACGCGTAGTGATCGAGGAATGGAGGCGGCACTACAACTCCGTTCGCCCACATTC
AAGCCTAAACAACATAACGCCTGAACACTTTTGTCGGCAGTATGGAAAAAAACTGAACCGTGGGGAAACCATCAAGAATTGAGTGGTCCGAAGTTTCCCG
GCAGGTCA
ATGGTCGGCATTCTGCGAGAAGCTGACCGTAGTCCAGTGGCCCAGGTGGCCAAGAAGCATGGAATCAGCGAGCAGACGATCTACACATGGCGCCAGCGGT
TCGCAGGCATGTCCGCCGATGACGTGAAGCGGCTACGCCTGCTGGAACAAGAGAACACGCGGCTGAAGAAGATACTTGCGGAACGGGACCTTGAAATCGA
GGTCATGAAGGAAATCGCCACAAAAAAATGGTAGGCGCACCCGTCCGACGCATCCAGGTGGCATACGCTAGGAGTCGCGGGCTTTCACAACGCAGGGCGT
GTGCGCTGTTATCCACTTCCCGGTCGTCGCTCCACTACGAGTCACGGCTGGAGGCTCGGGACAAGCCCCTGATGGCGGCGATGTCAGGTCTAGCTGCGGC
GTATCCGCGCTTTGGATATCGCCGGATCAACGTGTTCATGGAGCGTCTGGGTCATGTCATGGGGGCCGACAAGGCGTTCCGGCTTTGATGCAAGGCCGGG
TTGCAGGTGCCCAGAAAGCGGCCTCGGAAGCGGATTGCGGCGTCCCGTCCGCGACCACAACTGCCGATGGGTGCAAACGAACTGTGGGCGTACGACTTTG
TCTACGACGCCTGTGCAAATGGTCAGCCGATAAAATGCCTGACCGTGGTGGACGAATACACGCGCGAATGCCTGGCTATAGACGTTGCCGGGAGCATCAG
GTCGGGCCGGGTGATTGAGGTGCTGTCCCGCCTGATTAGTGAACGTGGAGCCCCTCTGAGCCTACGTTCTGACAACGGACCGGAGTTCGTGTCGAAGGCA
CTGCTCAGATGGGCGGCTCGGGAGTCTCTGAATCTGGCTCTGATTGAGCCTGGCAAGCCCTGGCAGAACGGTTTGAACGAGAGTTTTAATGGCAAATTTC
GCGACGAATGTCTGTCAATGGAATGGTTCCGGTGTCGGGACGAGGCACGCGTAGTGATCGAGGAATGGAGGCGGCACTACAACTCCGTTCGCCCACATTC
AAGCCTAAACAACATAACGCCTGAACACTTTTGTCGGCAGTATGGAAAAAAACTGAACCGTGGGGAAACCATCAAGAATTGAGTGGTCCGAAGTTTCCCG
GCAGGTCA
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 | |
---|---|---|---|---|---|
264 bp | 87 aa | 71 | 334 | + | No |
Description : First part of the transposase
ORF sequence :
MKKGRFSEEQMVGILREADRSPVAQVAKKHGISEQTIYTWRQRFAGMSADDVKRLRLLEQENTRLKKILAERDLEIEVMKEIATKKW
Blast result :ORF 2
Length | Begin | End | Strand | Fusion ORF | |
---|---|---|---|---|---|
888 bp | 295 aa | 295 | 1182 | + | No |
Description : Second part of the transposase
ORF sequence :
NRGHEGNRHKKMVGAPVRRIQVAYARSRGLSQRRACALLSTSRSSLHYESRLEARDKPLMAAMSGLAAAYPRFGYRRINVFMERLGHVMGADKAFRL*CK
AGLQVPRKRPRKRIAASRPRPQLPMGANELWAYDFVYDACANGQPIKCLTVVDEYTRECLAIDVAGSIRSGRVIEVLSRLISERGAPLSLRSDNGPEFVS
KALLRWAARESLNLALIEPGKPWQNGLNESFNGKFRDECLSMEWFRCRDEARVVIEEWRRHYNSVRPHSSLNNITPEHFCRQYGKKLNRGETIKN
AGLQVPRKRPRKRIAASRPRPQLPMGANELWAYDFVYDACANGQPIKCLTVVDEYTRECLAIDVAGSIRSGRVIEVLSRLISERGAPLSLRSDNGPEFVS
KALLRWAARESLNLALIEPGKPWQNGLNESFNGKFRDECLSMEWFRCRDEARVVIEEWRRHYNSVRPHSSLNNITPEHFCRQYGKKLNRGETIKN
Blast result :ORF 3
Length | Begin | End | Strand | Fusion ORF | |
---|---|---|---|---|---|
1112 bp | 370 aa | 71 | 1182 | + | Yes |
Chemistry : DDE
ORF sequence :
MKKGRFSEEQMVGILREADRSPVAQVAKKHGISEQTIYTWRQRFAGMSADDVKRLRLLEQENTRLKKILAERDLEIEVMKEIATKKMVGAPVRRIQVAYA
RSRGLSQRRACALLSTSRSSLHYESRLEARDKPLMAAMSGLAAAYPRFGYRRINVFMERLGHVMGADKAFRL*CKAGLQVPRKRPRKRIAASRPRPQLPM
GANELWAYDFVYDACANGQPIKCLTVVDEYTRECLAIDVAGSIRSGRVIEVLSRLISERGAPLSLRSDNGPEFVSKALLRWAARESLNLALIEPGKPWQN
GLNESFNGKFRDECLSMEWFRCRDEARVVIEEWRRHYNSVRPHSSLNNITPEHFCRQYGKKLNRGETIKN
RSRGLSQRRACALLSTSRSSLHYESRLEARDKPLMAAMSGLAAAYPRFGYRRINVFMERLGHVMGADKAFRL*CKAGLQVPRKRPRKRIAASRPRPQLPM
GANELWAYDFVYDACANGQPIKCLTVVDEYTRECLAIDVAGSIRSGRVIEVLSRLISERGAPLSLRSDNGPEFVSKALLRWAARESLNLALIEPGKPWQN
GLNESFNGKFRDECLSMEWFRCRDEARVVIEEWRRHYNSVRPHSSLNNITPEHFCRQYGKKLNRGETIKN
Blast result :
Comments
ISDvu3 is 84% aa similar to ISBp1.
There is a STOP codon in the ORFB and the transposase, the transposase is probably not active. The authors said that this gene contains a premature stop which is not the result of sequencing error
There is a STOP codon in the ORFB and the transposase, the transposase is probably not active. The authors said that this gene contains a premature stop which is not the result of sequencing error
References
1] ISfinder annotation (2010)
2] Heidelberg,J.F., Seshadri,R., Haveman,S.A., Hemme,C.L., Paulsen,I.T., Kolonay,J.F., Eisen,J.A., Ward,N., Methe,B., Brinkac,L.M., Daugherty,S.C., Deboy,R.T., Dodson,R.J., Durkin,A.S., Madupu,R., Nelson,W.C., Sullivan,S.A., Fouts,D., Haft,D.H., Selengut,J., Peterson,J.D., Davidsen,T.M., Zafar,N., Zhou,L., Radune,D., Dimitrov,G., Hance,M., Tran,K., Khouri,H., Gill,J., Utterback,T.R., Feldblyum,T.V., Wall,J.D., Voordouw,G. and Fraser,C.M. (2004) Nat. Biotechnol. 22 (5), 554-559
2] Heidelberg,J.F., Seshadri,R., Haveman,S.A., Hemme,C.L., Paulsen,I.T., Kolonay,J.F., Eisen,J.A., Ward,N., Methe,B., Brinkac,L.M., Daugherty,S.C., Deboy,R.T., Dodson,R.J., Durkin,A.S., Madupu,R., Nelson,W.C., Sullivan,S.A., Fouts,D., Haft,D.H., Selengut,J., Peterson,J.D., Davidsen,T.M., Zafar,N., Zhou,L., Radune,D., Dimitrov,G., Hance,M., Tran,K., Khouri,H., Gill,J., Utterback,T.R., Feldblyum,T.V., Wall,J.D., Voordouw,G. and Fraser,C.M. (2004) Nat. Biotechnol. 22 (5), 554-559