Extended Data Fig. 1: Distribution and identity of flavin and molybdopterin reductases in three taxonomic families.
From: Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration
Phylogenetic trees constructed with representative genomes from each Genome Taxonomy Database (GTDB) species in (a) Eggerthellaceae (88 genomes, 2387 amino acid sites), (b) Burkholderiaceae (1510 genomes, 2379 amino acid sites), and (c) Erysipelotrichaceae (116 genomes, 2464 amino acid sites). Each maximum likelihood tree was constructed based on a concatenated alignment of 16 ribosomal proteins under an LG + I + G4 model of evolution. The numbers of flavin (blue) and molybdopterin (red) reductases with a computationally predicted signal peptide in each genome are graphed on the outer ring of the trees. (d) Flavin reductase pangenomes of E. lenta, S. wadsworthensis, and H. filiformis. For each pangenome, the inner concentric layers represent unique genomes while the radial elements represent gene cluster presence (darker color) or absence (lighter color) across the genomes. The outermost concentric circle, ‘Max num paralogues,’ indicates the maximum number of paralogues (defined as reductases with ~60% sequence identity) one genome contributes to the gene cluster. The second outermost circle, ‘SCG clusters,’ indicates single-copy core reductase that is, gene clusters for which every genome contributed exactly one gene. Genomes (inner concentric layers) are clustered by the presence/absence of reductase gene clusters. All vs all genome average nucleotide identity is depicted in the heat map above the genome concentric layers.
