Dealing with variable positions in aligned sequences. A consensus that chooses only the most frequently occurring amino acid at a given column of an alignment (e.g., that from the Jalview applet of Clustal W) is best for indicating highly conserved residues, but does not give any consensus value for variable positions (such as those circled). B) A PCP-consensus for the same sequences selects the amino acid that is most similar in properties to all others in the set.
Schein et al. BMC Bioinformatics 2012 13(Suppl 13):S9 doi:10.1186/1471-2105-13-S13-S9