Alignment of MAP kinase cascades. Alignment of BioModels 9  and 11  as shown in Figure 4. The two alignments based on inferred similarities contain previously unmatched pairs (E2, RAFPH), (P_KKK, RAFp), and (KKPase, MEKPH) and some previously false matches are swapped. These incorrect matches resulted from the fact that elements represent proteins in different phosphorylation states but carry the same annotations. The inferred similarity measures differ in two details: the matching of RAF and RAFpRAFPH, which is correctly predicted from similarity propagation and the matching of Reaction19 and Reaction25, which is correctly obtained from feature propagation (data not shown).