Protein families and their evolution-a structural perspective.

@article{Orengo2005ProteinFA,
  title={Protein families and their evolution-a structural perspective.},
  author={Christine A. Orengo and Janet M. Thornton},
  journal={Annual review of biochemistry},
  year={2005},
  volume={74},
  pages={
          867-900
        }
}
We can now assign about two thirds of the sequences from completed genomes to as few as 1400 domain families for which structures are known and thus more ancient evolutionary relationships established. About 200 of these domain families are common to all kingdoms of life and account for nearly 50% of domain structure annotations in the genomes. Some of these domain families have been very extensively duplicated within a genome and combined with different domain partners giving rise to different… 
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The obtained cluster map shows that while some highly populated folds indeed appear to have evolved convergently, most domains of the same fold arose from an ancestral prototype, revealing that proteins are much less polyphyletic than previously assumed.
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TLDR
It was shown for 18 diverse representatives from all eukaryotic kingdoms that a pooled analysis of the tendencies for co-occurrence or avoidance of protein domains is indeed feasible, and large scale patterns of similarities and differences of domain contains between phylum-level or even higher level taxonomic groups are highlighted.
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TLDR
This chapter reviews the current research on how protein domain architectures evolve and examines whether all known cases of a given domain architecture can be assumed to have a single common origin (monophyly) or have evolved convergently (polyphyly).
The FGGY Carbohydrate Kinase Family: Insights into the Evolution of Functional Specificities
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A detailed model of the evolution of the FGGY kinase family is provided and it is shown that only combined molecular and phylogenetic approaches can help reconstruct a full picture of functional diversifications in such diverse families.
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