Sequence-based mutation analysis BCKDHA protocol
Pymol
Notice that our BCKDHA protein contains a signal peptide at the beginning of the sequence, which was included in all the SNP predictions and the mutation analysis. For visualizing a PDB file was used, which does not contain information about the signal petide. The length of the signal peptide (45 aa) has to be considered, when selecting the mutation positions in pymol. (For all mutation positions 45 aa had to be subtracted). As one mutation (G29E) was chosen which occurs in the signal peptide, no pymol visualization of this mutation was possible.
The visualization of the mutated residues was accomplished following the tutorial in the pymol wiki([1]). Example for mutation Q80E:
- load PDB file '1U5B:A'
- zoom resi 80
- Wizard -> Mutagenesis
- select resi 80
- No mutation -> select resultant residue
- Click Apply, Done
PSIBLAST
SIFT
SIFT was run with default parameters (Selected databse to search: UniRef90 2011 Apr, Median conservation of sequences: 3.00, Remove sequences more then 90 percent identical to query.)
