Extended Data Fig. 1: Unrooted maximum-likelihood phylogeny of representative NrdF (RNR subclass Ib radical-generating subunit) sequences.

All RefSeq NrdF sequences were clustered at 75% identity to reduce redundancy and a maximum-likelihood phylogeny was estimated. Sequences with non-canonical amino acids in the positions involved in coordinating the metal centre of the enzyme formed a well-supported clan in the NrdF2 group of sequences. We identified two variants, one in which three of the glutamates were replaced by glutamine, serine and lysine (NrdF2.QSK) and the other in which they were replaced by valine, proline and lysine (NrdF2.VPK). Both variants thus have a substitution of a lysine for the normally metal-bridging glutamine (residue 213 in M. florum NrdF2.VPK). Together, the two variants form a well-supported (96% bootstrap support) clan in the phylogeny inside the NrdF2 diversity. The NrdF2.VPK clan seems to be derived from the NrdF2.QSK clan. Behind the sequences in the tree are a set of sequences that are more than 75% identical to each represented sequence. The VPK and QSK sequences in the phylogeny represent 138 and 182 sequences in RefSeq, respectively.