Fig. 3

Genomic neighborhoods for the clades of predicted proteins belonging to the COG1009 (NADH:ubiquinone oxidoreductase of type 1, NuoL subunit, and Na⁺/H⁺ antiporter, MnhA subunit). Typical genomic neighborhoods are shown for the top and bottom clades of the tree that contain sequences of well-studied proteins. A set of 177 proteins belonging to a reduced but representative set of 124 genomes was aligned with the MUSCLE software [5]. The multiple alignment was verified manually and conserved blocks (total 238 positions) were used for the phylogenetic tree construction with the MEGA 7 software [17]. Bootstrap support values calculated from 100 iterations are shown on the branches. Red arrows correspond to the proteins that belong to COG3002