Difference between revisions of "Part:BBa K2255018:Design"

 
 
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===Design Notes===
 
===Design Notes===
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As  D3 and the signal sequence are both the best conserved part from the attachment protein. So with protein global alignment (Needleman-Wunsch alignment), from two or three sequence at one time, we were eventually able to determinate D1 and D2.
 
  
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The domain 3 (D3) and the signal sequence are both the best conserved part from the attachment protein. Using a global protein alignment (Needleman-Wunsch and [https://static.igem.org/mediawiki/parts/5/52/T--Aix-Marseille--alignement.pdf MUSCLE alignments]), using two or three sequence at one time, we were eventually able to determinate domain 1 (D1) and domain 2 (D2) from XacF1.
  
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We were able to found D1 and D2 domains because each domain is separated by a flexible sequence <ref>Heilpern, A. J. & Waldor, M. K. pIIICTX, a predicted CTXphi minor coat protein, can expand the host range of coliphage fd to include Vibrio cholerae. J. Bacteriol. 185, 1037–1044 (2003).</ref>. Then we retrotranslate this sequence in a nucleotidic sequence and we used iDT to optimise this sequence for ''E.coli'' production.
  
 
===Source===
 
===Source===

Latest revision as of 14:28, 6 October 2017


p3_X.fuscans (Rfc25)


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 223
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

The domain 3 (D3) and the signal sequence are both the best conserved part from the attachment protein. Using a global protein alignment (Needleman-Wunsch and MUSCLE alignments), using two or three sequence at one time, we were eventually able to determinate domain 1 (D1) and domain 2 (D2) from XacF1.

We were able to found D1 and D2 domains because each domain is separated by a flexible sequence [1]. Then we retrotranslate this sequence in a nucleotidic sequence and we used iDT to optimise this sequence for E.coli production.

Source

From the genomic sequence of XacF1.

References

  1. ↑ Heilpern, A. J. & Waldor, M. K. pIIICTX, a predicted CTXphi minor coat protein, can expand the host range of coliphage fd to include Vibrio cholerae. J. Bacteriol. 185, 1037–1044 (2003).