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Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes

Figure 3

Bidirectional Best Hits of crp and fnr Are Not Orthologs

We show selected clades from a phylogenetic tree of all BBHs of E. coli crp and E. coli fnr. For each gene, we show whether it is a BBH of crp or of fnr and what genome it is from. (The genome names include strain identifiers.) For each intermediate node, we show the bootstrap score (out of 100). The mixture of putative “crp” and “fnr” genes within well-supported clades shows that one or both assignments are incorrect. We also show which taxonomic group the genomes belong to. Except for the boxed Cyanobacteria, each clade in the gene tree corresponds to a taxonomic group in the species tree, which confirms that the gene tree is accurate and that the BBHs are misleading.

Figure 3

doi: https://doi.org/10.1371/journal.pcbi.0030175.g003