Use of the Superfamily Principle (transitivity rule) to establish homology: If A and B are homologous, B and C are homologous, and C and D are homologous, then A is homologous to D.

aThese comparison scores are insufficient to establish homology.Families being compared are presented in column 1. Uniprot IDs are provided in columns 2–5. When a Uniprot accession number is unavailable, an NCBI accession number is provided. Comparison scores, expressed in standard deviations (S.D.), are provided in columns 6–9. Columns 6–8 allow establishment of homology. Column 9 gives the value determined when A is compared to D directly. For example, in a comparison between LysE and RhtB, Protein A and Protein D are query proteins from each respective family. Protein B is a homologue of Protein A. Protein C is a homologue of Protein D. Comparisons with the negative control, the Mitochondrial Carrier (MC) family, are provided below the double-lined border.