Additional file 1: of Uncovering the trimethylamine-producing bacteria of the human gut microbiota

Neighbor-joining trees of all cutC (A) and cntA (B) protein sequences derived from the established databases. The phylogenetic position of the carrier is indicated on the class level by a color code except for cntA sequences from Proteobacteria, which are shown at the genus level. CutC sequences encoded by members of the genus Clostridium XIVa are indicated as well. On the right, neighbor-joining trees presented in a radial layout encompassing all unique protein sequences from our databases (cutC (C) and cntA (D) highlighted in gray) together with sequences below the set HMM cutoff threshold that were included in FrameBot analysis are shown. Sequences encoding a different function than cutC and cntA (based on uniprot ( http://www.uniprot.org )) are shown in pink. For cntA, 34 unique proteins that were above the HMM similarity cutoff, but not included in our database due to their high phylogenetic distance to biochemically verified cntA sequences, are highlighted by the orange line (D). A: 1,2-propanediol dehydratase (WP_007885173); B: B12-independent glycerol dehydratase (AFH58722); C: Benzylsuccinate synthase alpha subunit (O87943); D: Formate acetyltransferase (P09373); E: 4-hydroxyphenylacetate decarboxylase (Q18CP5); a: choline monooxygenase precursor (AAB52509); b: choline monooxygenase (BAF93188); c: choline monooxygenase (CAE17671); d: 3-chlorobenzoate-3,4-dioxygenase oxygenase subunit (Q44256); e: toluate 1,2-dioxygenase large subunit (AAA26047); f: anthranilate dioxygenase large subunit (AAC34813). (PDF 612 kb)