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