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BLAST searches of the archaeal genome sequences with the yeast protein sequences failed to identify any homologs of these eukaryotic proteins in Archaea, but more sophisticated searches using PSI-BLAST identifed a homolog of Pop5; this gene in M. thermoautotrophicus is ORF 687, i.e. Mth687. Pushing the analysis even harder resulted in the identification of homologs of Rpp1 (Mth688, the gene adjacent to the Pop5 homolog), Pop4 (Mth11), and Rpr2 (Mth1618). Homologs of these genes are found in other archaeal genomes, and were afterwards assigned by Eugene Koonin at the NCBI to clusters of orthologous genes (COGs) with their eukaryotic homologs.

So the question becomes, are these archaeal proteins that are vaguely similar to eukaryotic nuclear RNase P proteins really RNase P subunits in Archaea?