Fig. 1
Approach for selection of candidate transporters  (steps 1, 2 and 3), and neighbor-joining distance tree of top 15 highest HMMxylT scoring proteins from A. niger and T. reesei. Functionally validated xylose transporters were retrieved to train a HMMxylT, and used to analyze the in silico proteomes of A. niger and T. reesei. An analysis of the phylogenetic relationships of the top-scoring candidate transporters, taking into account the available literature, allowed the selection of candidate transporters that were subsequently characterized. Bootstrap values are indicated, nodes with bootstrap values <75 % are collapsed. Numbers indicate protein ID in JGI online genomes of A. niger ATCC1015 and T. reesei v2.0 [50, 66]. Proteins selected for further biochemical characterization are indicated in bold with protein names in brackets. AN_, A. niger; TR_, T. reesei; asterisks, previously experimentally validated transporters; hash symbol, the presence of a XlnR-binding motif as suggested by van Peij et al. [67] in the 1-kb upstream region of the encoding gene