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.
- 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