Skip to main content

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]