Schematization of the Different Levels
| Scale | Levels | Description | |
| Single-gene | Traditional ribosomal | Nucleotide sequence | Based on the small and large subunit ribosomal rRNA |
| Individual orthologs | Protein sequence | Based on a variety of established orthologous proteins | |
| Partial-proteome (multi-gene) | Ortholog occurrence | Protein function | Based on the occurrence of specific orthologs in the proteome |
| Protein fold occurrence | Protein structure | Based on the occurrence of specific protein folds in the proteome | |
| Entire genome | Amino acid frequency | Proteome composition | Based on frequency of single amino acids in the entire genome |
| Dinucleotide frequency | Genome composition | Based on frequency of pairs of adjacent nucleotides in entire genome | |
[i] This table delineates the three levels on which we compared the microbial genomes. On the single-gene level, both ribosomal RNA and orthologous proteins were used for phylogenetic analysis. These used sequence-based methods for tree construction. The second level uses the presence or absence of orthologous protein groups or protein folds. Because some parts of the genome are assigned neither to a protein fold nor to an ortholog, we call this scale “partial proteome.” This scale is based on both protein function and protein structure. The most encompassing scale uses dinucleotide and amino acid composition as a basis for genome comparison. The entire genome is considered.