An original repertoire of candidate effector proteins in P. ultimum. (a) The number of candidate RXLR effectors estimated by Hidden Markov Model (HMM) searches of predicted proteins with amino-terminal signal peptides. The numbers of false positives were derived from HMM searches of the permutated protein sequences. (b) The number of candidate RXLR effectors discovered by motif searching. The search was performed on the total set of six-frame translated ORFs from the genome sequences that encode proteins with an amino-terminal signal peptide. The motif RXLR and two more degenerate motifs, RXLX or RX[LMIFY][HKR], were required to occur within 100 amino acids of the amino termini. (c) The typical architecture of a YxSL[RK] effector candidate inferred from 91 sequences retrieved from P. ultimum, three Phytophthora genomes and A. euteiches. (d) The YxSL[RK] motif is enriched and positionally constrained in secreted proteins in P. ultimum and Phytophthora spp. The top graph compares the abundance of YxSL[RK]-containing proteins among secreted and non-secreted proteins from four oomycete genomes. The middle and bottom graphs show the frequency of the YxSL[RK] motif among non-secreted and secreted proteins, respectively, according to its position in the protein sequence. (e) Cladogram based on the conserved motifs region of the 91YxSL[KR] proteins, showing boostrap support for the main branches.
Lévesque et al. Genome Biology 2010 11:R73 doi:10.1186/gb-2010-11-7-r73