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Table 1 A list of the fourteen modules that are lineage specific but also well conserved within eleven major archaeal lineages. A family was counted as having a signal peptide if at least 25% of its protein sequences were predicted to have a signal peptide prediction according to the SignalP software [32]. A family was counted as having a transmembrane helix if more than half of its protein sequences were predicted to have a transmembrane helix according to the TMHMM software [33]. Families were considered hypothetical if they have neither PFAM (Domain of Unknown Function domains were excluded) nor KEGG annotations (see the supplementary dataset - Table S3 for the full list of hypothetical families). Finally, a family was considered to have bacterial homologs if the family matched with protein sequences of at least ten distinct bacterial genomes (see the “Methods” section). The core module 1 is included as a comparison

From: Conserved and lineage-specific hypothetical proteins may have played a central role in the rise and diversification of major archaeal groups