Measures of genome evolution: operon conservation versus conservation of gene repertoire and protein sequences. Alignments including apparent orthologs (bidirectional best hits) were used in both plots (E < 0.1). (A) Gene string conservation versus co-occurrence in clusters of orthologous genes (COGs). The co-occurrence coefficients for genome alignments and for the COGs were calculated as indicated in Methods. (Dark-blue diamonds) Archaeal-bacterial comparisons, (light-blue crosses) bacterial–bacterial comparisons, (red squares) archaeal–archaeal comparisons. (B) Gene string conservation versus sequence identity level between probable orthologs. Horizontal axis: median fraction of identical amino acid residues among probable orthologs. The other designations are as in A.