Figure 1/S1: Ribosomal protein alignment - Metagenomic Evidence for the Presence of Comammox Nitrospira-like bacteria in a Drinking Water System

Alignment used to construct RAxML (1) based maximum likelihood phylogenetic tree corresponding to the radial cladogram in Figure 1A in the main manuscript and annotated tree in the supplementary material Figure S1. 16 syntetic ribosomal proteins (2) were aligned separately with correponding sequence from the Nitrospira metagenome bin using muscle (3) . Each protein alignment was trimmed using trimal with the gappyout flag (4) and the trimmed alingments were concantenated to create a superalignment using FasconCAT (5). 1. Stamatakis A. 2014. RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Bioinformatics 30: 1312-1313. doi: 10.1093/bioinformatics/btu033. 2. Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen JA, Banfield JF. 2013. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun 4. doi: 10.1038/ncomms3120 3. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792-1797 4. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972-1973. doi: 10.1093/bioinformatics/btp348 5. Kück P, Meusemann K. 2010. FASconCAT: Convenient handling of data matrices. Molecular Phylogenetics and Evolution 56:1115-1118.