AMPK Methods and Protocols

reason at this level to assume that the two proteins have

diverged in their functionality.

Feature Architecture Similarity (FAS) score calculation

integrated into HaMStR-OneSeq.

2. The FAS scoring is natively implemented in the HaMStR-
   OneSeq workflow (seesteps 19– 21 in Subheading3.3). For
   orthologs predicted with this tool, no further steps are
   required. The relevant results are stored in three files whose
   contents can later be visualized with the PhyloProfile applica-
   tion (seeSubheading3.5): (1)seedProteinName_1.matrix, this
   file is the phylogenetic profile vector for the query protein;
   (2) seedProteinName.extended.profile, this file provides the
   ortholog ids along with their FAS score; (3) seedProtein-
   Name_1.domains, this file contains information about the
   domain architectures of the seed protein and of the
   corresponding orthologs.

Fig. 5Feature architecture of human PRKAA. The plot displays the results of an InterProScan [27] analysis of
human PRKKA1 (AMP-activated protein kinase alpha subunit, UniProt ID Q13131)

Tracing AMPK Evolution 125