Figure 3

Examples of motif misalignments in multiple sequence alignments calculated with ClustalW. Certain linear motifs have characteristics that make them prone to be wrongly aligned by multiple sequence alignment algorithms. This is the case for repetitive motifs that occur in different number of copies per sequence, and often for those motifs located in the protein C-terminus. On the left, the repetitive instances of the DP[FW] epsin motif responsible for the binding with the AP2 adaptor complex. On the right, the C-terminus PTS1 motif involved in the targeting of the eukaryotic catalases to the peroxisome.