More than the sum of their parts: On the evolution of proteins from peptides

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ECOD: An Evolutionary Classification of Protein Domains (2014, background): “Where domains had no confident Pfam assignment, allversus-all HHsearch-based complete linkage clustering was used to generate an F-group [32] where all domains shared 90% HHsearch probability.”
De novo identification of highly diverged protein repeats by probabilistic consistency (2008, background): “These results further support the ‘ancient peptide hypothesis’, which posits that modern proteins arose by recombination and fusion from a small set of fragments (ancient peptides) (Lupas et al., 2001; Söding and Lupas, 2003).”
The evolutionary origin of orphan genes (2011, background): “Most of these folds were already present in the ancestral set of genes, and it has been suggested that they are derived from ancestral peptides that were active at the transition from the RNA to the protein worl”