Table 1.

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

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.