Extended Data Fig. 6 | Maximum-likelihood tree of Asgard archaea
urocanate hydratase. Urocanate hydratase (HutU) homologues were obtained
by BLASTp analysis of the Asgard archaea sequences against the UniProt
database (release 2019_06). Of homologues with sequence similarity ≥40% and
overlap ≥70%, representative sequences were selected using CD-HIT with a
clustering cut-off of 70% similarity (otherwise default settings were used).
Additional homologues with verified biochemical activity, sequence similarity
≥30% and overlap ≥70% were obtained by BLASTp analysis of the Asgard
archaea sequences against the UniProt/SwissProt database (2019_05).
Sequences were aligned using MAFFT v.7 with default settings and trimmed
using trimAl v.1.2 with default settings. The maximum-likelihood tree was
constructed using R AxML-NG using fixed empirical substitution matrix (LG),
4 discrete GAMMA categories, empirical amino acid frequencies from the
alignment and 100 bootstrap replicates. In total, 876 sites of the alignment
were used for tree construction.