Table 3 Bioinformatics tools and methods integrated into the Predector pipeline.

(A) Localisation

SignalP v3.0, 4.1g, 5.0b

Extracellular secretion via signal peptide. Both NN and HMM methods are run for v3.0. Eukaryotic types specified

^23,24,25

Deepsig commit 69e01cb

Extracellular secretion. *-k euk

²⁷

Phobius 1.01

Extracellular secretion

²⁶

LOCALIZER v1.0.4

Host sub-cellular localisation. Using predicted mature proteins from SignalP 5.0b. *-e -M

³⁴

ApoplastP v1.0.1

Apoplast-specific localisation

³⁵

DeepLoc v1.0

Sub-cellular localisation

²⁹

TargetP v2.0

Sub-cellular localisation. *-org non-pl

²⁸

TMHMM v2.0c

Membrane localisation via transmembrane domains. *-d

³⁰

(B) Effector-like properties

EffectorP v1.0, 2.0

Probabilistic prediction of effector likelihood

^31,32

EMBOSS: pepstats v6.5.7

Amino acid properties and frequencies

⁶⁵

(C) Functional annotation

HMMER (vs dbCAN v8) v3.2.1

Used to search dbcan

^60,66

MMSeqs2 v10-6d92c (vs PHIBase v4.9)

Used to search phibase. *--max-seqs 300 -e 0.01 -s 7 --num-iterations 3 -a

^40,55

MMSeqs2 v10-6d92c (vs known effectors in Supplementary Table S2)

*--max-seqs 300 -e 0.01 -s 7 --num-iterations 3 -a

⁵⁵

PfamScan (vs Pfam v33.1)

With active site prediction. *-as

⁶⁷