All eukaryotic protein sequences associated with different functions in KEGG (Kyoto Encyclopedia of Genes and Genomes, as of November 2021) were used to build representative hidden Markov models (HMMER/3.1), which were then searched against all prokaryotic genomes available on KEGG. Based on hits found across bacterial phyla, the following categories were assigned: Universal (shared with >50% bacterial phyla and archaea), Eu|Ar|Ba (shared with archaea and <50% bacterial phyla), Eu|Ar|Pr (shared with archaea and proteobacteria only), Eu|Ar (shared with Ar), Eu|Asgard (shared only with asgard archaea), Eu|non-Asgard (shared only with non-asgard archaea), Eu|Ba (shared with bacteria), Eu|Proteo (shared only with proteobacteria), Eu (not shared with any prokaryotes). Each box shows the percentage of protein families across these categories (x-axis) for the pathways analysed. For example, a substantial percentage of ribosomal proteins (bottom right) are shared between Eukaryote-Archaea or Eukaryote-Archaea-Bacteria, highlighting the host’s ribosomal contribution to eukaryotes. Proteins for other categories, however, are either predominantly eukaryote-specific or shared between eukaryotes and bacteria (e.g. glycotransferases or some proteins of autophagy). CMA, chaperone-mediated autophagy; CVT, cytoplasm to vacuolar targeting pathway.