Figure 3.

Maximum-likelihood NirK phylogeny. The phylogeny was inferred from 6,422 full-length NirK amino acid sequences using the LG+F+R10 model in IQ-TREE. Black circles on tree indicate nodes with SH-aLRT ≥ 80% and UFboot ≥ 95% support. Tips of tree are shaded according to clade, and data rings denote (i) phylum determined using GTDB-TK; (ii) presence of secondary nirK copies from other clades; (iii–ix) select NirK structural features. The outgroup, consisting of 367 multicopper oxidases derived from Cyanobacteria and Thermoprotetota genomes, is collapsed for clarity; clades are numbered and lettered following Wei et al. [29] and Bonilla-Rosso et al. [28] as much as possible, starting with the “canonical” Clade 1a; the star marks the location of the AniA NirK proteins from N. gonorrhoeae. [48]