Difference between revisions of "Part:BBa K2255005:Design"
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===Design Notes=== | ===Design Notes=== | ||
| − | + | The domain 3 and the signal sequence are both the best conserved part from the attachment protein. Using a global protein alignment (Needleman-Wunsch alignment), using two or three sequence at one time, we were eventually able to determinate D3 from M13. | |
This is the complete amino acid sequence of M13 protein 3: | This is the complete amino acid sequence of M13 protein 3: | ||
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</code> | </code> | ||
| − | We choose to only keep the | + | We choose to only keep the D3 of this protein: |
<code> | <code> | ||
| − | + | AETVESCLAKSHTENSFTNVWKDDKTLDRYANYEGCLWNATGVVVCTGDETQCYGTWVPIGLAIPENEGGGSEGGGSEGGGSEGGGTKPPEYGDTPIPGYTYINPLDGTYP | |
| − | + | PGTEQNPANPNPSLEESQPLNTFMFQNNRFRNRQGALTVYTGTVTQGTDPVKTYYQYTPVSSKAMYDAYWNGKFRDCAFHSGFNEDLFVCEYQGQSSDLPQPPVNAGGG | |
</code> | </code> | ||
| − | We were able to found it because each domain is separated by a flexible sequence composed of Glycine and Serine <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. | + | We were able to found it because each domain is separated by a flexible sequence composed of Glycine and Serine <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 02:46, 2 November 2017
Domain 3 of p3 from M13 (Rfc25)
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
Design Notes
The domain 3 and the signal sequence are both the best conserved part from the attachment protein. Using a global protein alignment (Needleman-Wunsch alignment), using two or three sequence at one time, we were eventually able to determinate D3 from M13.
This is the complete amino acid sequence of M13 protein 3:
MKKLLFAIPLVVPFYSHSAETVESCLAKPHTENSFTNVWKDDKTLDRYANYEGCLWNATGVVVCTGDETQCYGTWVPIGLAIPENEGGGSEGGGSEGGGSEGGGTKPPEYG
DTPIPGYTYINPLDGTYPPGTEQNPANPNPSLEESQPLNTFMFQNNRFRNRQGALTVYTGTVTQGTDPVKTYYQYTPVSSKAMYDAYWNGKFRDCAFHSGFNEDPFVCEYQ
GQSSDLPQPPVNAGGGSGGGSGGGSEGGGSEGGGSEGGGSEGGGSGGGSGSGDFDYEKMANANKGAMTENADENALQSDAKGKLDSVATDYGAAIDGFIGDVSGLANGNGA
TGDFAGSNSQMAQVGDGDNSPLMNNFRQYLPSLPQSVECRPFVFSAGKPYEFSIDCDKINLFRGVFAFLLYVATFMYVFSTFANILRNKES
We choose to only keep the D3 of this protein:
AETVESCLAKSHTENSFTNVWKDDKTLDRYANYEGCLWNATGVVVCTGDETQCYGTWVPIGLAIPENEGGGSEGGGSEGGGSEGGGTKPPEYGDTPIPGYTYINPLDGTYP
PGTEQNPANPNPSLEESQPLNTFMFQNNRFRNRQGALTVYTGTVTQGTDPVKTYYQYTPVSSKAMYDAYWNGKFRDCAFHSGFNEDLFVCEYQGQSSDLPQPPVNAGGG
We were able to found it because each domain is separated by a flexible sequence composed of Glycine and Serine [1]. Then we retrotranslate this sequence in a nucleotidic sequence and we used iDT to optimise this sequence for E.coli production.
Source
The initial sequence came from E.coli M13 filamentous phages. But we modified the sequence with iDT optimisation codon.
References
- ↑ 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).