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Table 3 Databases and methods used to annotate protein-coding genes in the 10 genomes analyzed

From: Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens

Name of Database Function Method Parameters Citation
Blast2GO Protein homology annotation BLASTP e-value < 10-3 [122]
Pfam Conserved domain annotation HMM e-value ≤ 1e-3 [123]
CAZYmes Analysis Toolkit (CAT) CAZyme family annotation BLASTP Default [128]
antiSMASH Secondary metabolite clusters HMM Default (Eukaryotic) [64]
fPoxDB Fungal peroxidase family annotation HMM e-value ≤ 1e-5 [56]
SignalP 4.1 Presence and location of signal peptide cleavage sites Neural network Default (Eukaryotic) [64]
The Cytochrome P450 Homepage Cytochrome P450 monooxygenase family annotation BLASTP e-value ≤ 1e-5 [129]
Transporter Classification Database Classification of Membrane Transport Proteins BLASTP e-value ≤ 1e-5 [130]
Pathogen-Host Interaction (PHI) database Experimentally tested genes for pathogen-host interaction BLASTP e-value ≤ 1e-5 [46]