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Pearson's correlation coefficients were used to investigate the relationship between domain evolution and protein family evolution (Table 3).
Systematic studies of protein evolution, especially those that examine the relationships between domain evolution and protein family evolution have been limited by a dearth of sequence and functional data at the genomic level.
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These studies highlight the potential to glean important associations between domain evolution, protein family evolution, and species adaptation from systematic studies of protein and genomics databases.
By reconstructing the evolution of protein families and domains over lineages that span the Metazoa which included all three major groups and multiple species within each group, for the first time we were able to quantify the relationship between protein family evolution and domain evolution, and examine the effects of domain shuffling in a lineage specific manner.
This feature makes domain architecture content, like domain content [ 9], an ideal probe to study protein domain evolution and genome evolution.
This work provided a systematic analysis of both protein family evolution and domain evolution at the genomic level.
Detailed analysis of alignments using plots of Dayhoff scores confirmed the difference between mouse and human N domain evolution.
These insights include the formation of novel domain combinations and their evolution, the divergence of one superfamily into several families, and the general trends in domain evolution.
Our observations regarding the relationship between domain insertions and the structure, function and evolution of proteins have implications for protein engineering.
Fusion of domains in a multidomain protein results in substantial homogenization of the domain-specific evolutionary rates but significant differences between domain-specific evolution rates remain.
An extensional domain-relative approach introduces the distinction between "domain preserving" and "domain combining" reductions.
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