ISDvu3

  • Family IS3
  • Group IS407
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
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 flankDirect repeatRight flankDR Length
GGGGTCGATATCTTAAGAGC0

DNA sequence

TGACCTGCCCGGCACTTTTCAGACCAGCCGAAACTTGAGATAGGTTTCTCCCTCAACCACGAGGGAACCGATGAAAAAGGGACGATTTTCCGAAGAGCAG
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
LengthBeginEndStrandFusion ORF
264 bp87 aa71334+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MKKGRFSEEQMVGILREADRSPVAQVAKKHGISEQTIYTWRQRFAGMSADDVKRLRLLEQENTRLKKILAERDLEIEVMKEIATKKW

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
888 bp295 aa2951182+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

NRGHEGNRHKKMVGAPVRRIQVAYARSRGLSQRRACALLSTSRSSLHYESRLEARDKPLMAAMSGLAAAYPRFGYRRINVFMERLGHVMGADKAFRL*CK
AGLQVPRKRPRKRIAASRPRPQLPMGANELWAYDFVYDACANGQPIKCLTVVDEYTRECLAIDVAGSIRSGRVIEVLSRLISERGAPLSLRSDNGPEFVS
KALLRWAARESLNLALIEPGKPWQNGLNESFNGKFRDECLSMEWFRCRDEARVVIEEWRRHYNSVRPHSSLNNITPEHFCRQYGKKLNRGETIKN

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
1112 bp370 aa711182+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MKKGRFSEEQMVGILREADRSPVAQVAKKHGISEQTIYTWRQRFAGMSADDVKRLRLLEQENTRLKKILAERDLEIEVMKEIATKKMVGAPVRRIQVAYA
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
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