Fig. 4.

Phylogeny of Nitrospira ammonium transporters. The maximum likelihood tree is based on a manually refined muscle (Edgar 2004) protein alignment and was calculated with RaxML (Stamatakis 2014) on the CIPRES Science Gateway (Miller et al. 2010) using the WAG substitution and PROTCAT rate heterogeneity models and 100 bootstrap replicates. A 10% conservation filter was used, resulting in 457 alignment positions. Rh-type transporters of comammox Nitrospira and selected reference organisms were used to root the tree. The arrow indicates the position of the outgroup. The scale bar corresponds to 50% estimated sequence divergence. Numbers in brackets reflect the number of sequences contained in the respective sequence group