Before revision:  Among the few genes lost are both eukaryotic clpB orthologs, HSP104 and HSP78  , which encode amyloid disaggregases.
After revision:  These genes suggest a coherent pattern of gene loss from which the biological and ecological context of animal origins can be inferred. First, we find that a large number of genes for multiple biosynthetic pathways were lost in the stem-metazoan lineage. Second, we find that of all the essential amino acid pathway genes absent in animals, only the biosynthetic pathways for the branched chain amino acids are also absent in choanoflagellates, the sister group to animals. Third, we find only a few conserved genes lost in the stem-metazoan lineage that do not encode metabolic enzymes, and these include the eukaryotic clpB genes, HSP78 , which encode amyloid disaggregases.