The procedure for predicting the functional consequences on the protein function is as follows (see Supp. Fig. S1 for a flow diagram detailing the procedure): the JackHMMER component of HMMER3 (one iteration with the optional –hand parameter applied; see Supp. Fig. S2) is used to search for homologous sequences within the UniRef90 [Suzek et al., 2007] database (November 2011). As part of this procedure, an ab initio HMM representing the MSA of homologous sequences (with Dirichlet mixtures [Sjölander et al., 1996]) is constructed and used. In conjunction, protein domain annotations from the SUPERFAMILY [Gough et al., 2001] (version 1.75) and Pfam [Sonnhammer et al., 1997] (Pfam-A and Pfam-B; version 26.0) databases are made. The relevant SUPERFAMILY and Pfam HMMs are then extracted only if and when the domain assignment is deemed significant (e-value ≤0.01) and the AAS maps onto a match state within the model.
