3. Genomic characterization of TS proteins
In order to characterize TS enzymes in Trichoderma spp. andB. bassiana we used a combination of different approaches: i) PTs
proteins were identified based on Pfam and Panther motifs, which in turn
enabled differentially identification of TCs proteins; ii) Conserved
aspartate-rich metal-binding motifs associated to Class I
(D[D/E]xx[D/E]) and Class II (DxDD) TS-folds (Gao, Honzatko, &
Peters, 2012) of mono- and bifunctional enzymes were identified
searching for profile Hidden Markov Models (pHMM) in the amino-acidic
sequences; iii) Substrate-specificity and putative functions were
assigned by phylogenetic analysis: Trichoderma spp. and B.
bassiana TS proteins were aligned by MAFFT v7.450 (Katoh et al., 2013)
along with TS proteins of known functions and described in literature
(Supporting Information Table S2 ). Phylogenetic tree was built
with: MrBayes (Ronquist & Huelsenbeck, 2003), FasTree v2.1.11 (Price,
Dehal, & Arkin, 2010) and PhyML v3.3.2 (Guindon et al., 2010). The best
substitution model was obtained using ProtTest (Abascal, Zardoya, &
Posada, 2005). Phylogenetic tree was reconstructed using the WAG + I
evolutionary model (Whelan & Goldman 2001). The probabilities and
bootstrap values threshold were 50%. Phylogenetic trees were visually
checked and topology conservation evaluated. Sequences used for
alignments and corresponding to each phylogenetic cluster identified
were individually screened for conserved domains using InterProScan as
described above.