Figure 1.
Enrichment of amino acids in effector N-termini.
Amino acids that are significantly enriched or depleted in the first 25 residues of effectors from the animal pathogen effector set and from the plant symbiont effector set (p-Value<0.05 in the one sided Mann-Whitney test in at least one of the sets). Frequencies are given as percentage of amino acids within the 25 first residues. Error bars represent one standard deviation in plus and one standard deviation in minus directions.
Table 1.
Performance of different classification algorithms for the prediction of TTSS effectors.
Table 2.
Most discriminating features between positive and negative instances.
Figure 2.
Exploration of position and length of the signal.
Exploration of optimal length of the signal (A) and begin position of a 15 amino acid long window (B). The AUC value for each length and begin position is plotted for the animal pathogen set (red) and the plant symbiont set (green).
Figure 3.
Taxonomic universality of the signal.
The y-axis denotes the achieved AUC value of EffectiveT3 when trained without the positive and negative samples from the taxonomic group denoted at the bottom of the x-axis and tested against this set. The performance on a randomly chosen set of positives and negatives having the same taxonomic composition is given for comparison.
Figure 4.
Overview of EffectiveT3 predictions in complete genomes from Gram-positive bacteria and archaea.
The figure shows the percentage of positive predictions in proteomes from Gram-positive bacteria and archaea, respectively, depending on the G+C content of the genomes. Linear fits are shown by trend lines in the colours of the respective data sets; attached are the coefficients of determination R2 of each fit. The individual results for all proteomes can be found in Table S11.
Figure 5.
Overview of EffectiveT3 predictions in complete genomes from Gram-negative bacteria with and without TTSS.
The figure shows the percentage of positive predictions in proteomes from Gram-negative bacteria with and without TTSS, depending on the G+C content of the genomes. The plot has been scaled as Figure 4 to facilitate comparison. Linear fits are shown by trend lines in the colours of the respective data sets; attached are the coefficients of determination R2 of each fit. The individual results for all proteomes can be found in Table S11.
Table 3.
Mapping of amino acids to property alphabets.