Extended Data Fig. 3: Network of putative non-redundant MGCs predicted by gutSMASH.
From: gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota
From all the unknown predicted MGCs, a redundancy filtering of 0.9 sequence similarity was applied using MMseqs2. From each cluster, two representatives were picked, and all representatives were used as input for BiG-SCAPE using the default cutoffs. The network contains 2,921 nodes and 7,474 edges. The MGCs have been classified into four different categories based on the key enzyme classes they code for. The GR (glycyl-radical) category is composed of MGCs that include pyruvate formate-lyase (PFL-like) and/or glycyl radical (Gly_radical), OD (oxidative decarboxylation) involves MGCs with at least one of the following Pfam domains: pyruvate ferredoxin/flavodoxin oxidoreductase (POR), pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg (POR_N), pyruvate:ferredoxin oxidoreductase core domain II (PFOR_II) and thiamine pyrophosphate enzyme, C-terminal TPP binding domain (TPP_enzyme_C). The flavoenzymes category is a combination of MGCs harbouring at least one of the custom-made BaiCD and BaiH pHMMs. HGD-D-related MGCs, as the name states, include enzymes matching any of the 2-hydroxyglutaryl-CoA dehydratase, D-component (HGD-D)-related pHMM domains.
