Fig. 2: Phylogeny of 1261 detected expressed TonB-dependent transporters in the metaproteome data, the 96 reference TBDT sequences with known substrates from ref. [65], and the peptidase exporter from ref. [66], divided into the four categories ascribed therein, namely DOM transporters, metals transporters, haemophore transporters, and siderophore transporters.

The three lobes (two blue, one yellow) are putative functional groupings. DOM group 1 includes 844 sequences, 64 associated with laminarin degrading CAZymes, 20 with alginate, 23 with alpha-glucan, 25 with fucose, mannose, or xylose-containing polymers, 53 associated with CAZymes where no substrate was predicted, 22 reference DOM transporters, and the peptidase transporter reference. DOM group 2 includes 338 proteobacterial sequences, 7 associated with laminarin degrading CAZymes, 17 with other CAZymes without substrate predicted, and 4 reference siderophore transporters. The putative non-DOM clade includes 182 sequences, none associated with CAZymes. Of those 182, 69 are reference sequences, all of them siderophore, haem, or metals transporters. Individual clades in the tree are arbitrarily labelled numerically for findability, and with letter codes indicating the types of sequences in that clade. B = sequences from Bacteroidetes, P = sequences from Proteobacteria, A = sequences from Actinobacteria, V = sequences from Verrucomicrobia; D = DOM transporter reference, E = exporter reference, H = haem transporter reference, Me = metals transporter reference, S = siderophore transporter reference; α = alpha-glucan transporter, L = laminarin transporter, M = mannose-rich polymer transporter. All clades can be associated with sequences in the data in Supplementary Table S3. Clades 3-PD and 9-BD correspond to the main PUL-containing clades of TBDTs, and thus the polysaccharide transporters are left out of the label encoding in favour of the expanded subtrees with additional detail. Clade 9-BD corresponds to the SusC-like proteins, identified by TIGR04056.