Figure 3
Multiple sequence alignments of representative sequences in the DUF4424 and YARHG families. The secondary structure of [PDB:4g2a], which corresponds to [UniProtKB:Q5ZTF2] is shown above the alignment, with alpha helices colored red and beta strands colored yellow. The secondary structure elements are numbered as in Figure 1. (A) Multiple sequence alignment of representative DUF4424 domain sequences. Sequences were chosen based on both domain architecture and taxonomic distribution. The following sequences contain a C-terminal YARHG domain: [UniProtKB:Q5ZTF2] (Legionella pneumophila), [UniProtKB:Q7P768] (Fusobacterium nucleatum). The following sequences all from different Proteobacterial classes contain only the DUF4424 domain: [UniProtKB:C6B3I8] (Rhizobium leguminosarum bv. trifolii), [UniProtKB:C6M949] (Neisseria sicca), [UniProtKB:E8RIM1] (Desulfobulbus propionicus), [UniProtKB:B5NMH4] (Salmonella enterica). [UniProtKB:Q64EJ4] contains a C-terminal CARDB domain (Archaea metagenomics). (B) Multiple sequence alignment of representative YARHG domains. The alignment has been split to show examples of the classical YARHG at the top and the YASKG subfamily at the bottom. The classical YARHG representatives are: [UniProtKB:B5CPT2] (Ruminococcus lactaris ATCC 29176), [UniProtKB:C3BHH4] (Bacillus pseudomycoides), [UniProtKB:C3WK84] (Fusobacterium sp. 2_1_31), [UniProtKB:C7NDL9] (Leptotrichia buccalis), [UniProtKB:D8E0N2] (Prevotella bryantii), [UniProtKB:E2N0N0] (Capnocytophaga sputigena), [UniProtKB:H0MP08] (Salmonella enterica subsp. enterica serovar Montevideo str), [UniProtKB:Q7P768] (Fusobacterium nucleatum subsp. vincentii), [UniProtKB:Q8XP49] (Clostridium perfringens), [UniProtKB:A9G0S1] (Phaeobacter gallaeciensis) The YASKG subfamily contains four conserved cysteine residues, that are marked by a gray circle below the column. The sequences shown for this subfamily are: [UniProtKB:B0VPK4] (Acinetobacter baumannii), [UniProtKB:C6RJI6] (Acinetobacter radioresistens), [UniProtKB:D0C4A2] (Acinetobacter sp. RUH2624), [UniProtKB:G7GH70] (Acinetobacter sp. NBRC 100985).