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The PCA map (Fig. 3, left) revealed a large difference in the clustering of domain genes and thus the differential coexpression of the gene cluster between ES and EB.
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The clustering of domains of unknown function indicates a conserved function among these bicupin homologues.
Towards this end we reconstructed a phylogenetic tree on the basis of entire FYVE domain from all FYVE protein sequences from viridiplantae and observed clustering of domains with signature ligand-binding site consensus patterns.
For example, polyproteins and their component proteins, or clusters of domain families partially sharing domain architecture.
Hierarchical clustering of these values shown in Figure 2B reveals clusters of protein domains that have evolved similarly across eukaryotes, indicated by the colors of each cluster of domains.
Fig. 2 shows the functional site coverage against a simple measure of superfamily diversity, namely the number of clusters of domains at 60% sequence identity.
There is evidence of clusters of domains with similar magnitude and direction of effect, in keeping with a previous report [ 5].
MDL plots generally take a shape that looks like the head and neck of a bird and contains three major clusters of domains.
It is part of a cluster of domains of the RyR2 that undergo conformational change when the channel is switched from the closed to the open state (22, 23).
The ~70-kDa signature structure of this family is a compact cluster of domains comprising four EF-hand motifs and a ZZ-domain, followed by a looser region with a propensity to form coiled-coils.
All newly-identified clusters of domains distinct from previously identified sequence families containing the β-GF were aligned and used to predict secondary structure with the JPRED program [ 53].
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