More Than 1,001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology
Figure 2
Histograms of average log probability per predicted transmembrane helix and per predicted signal peptide in Pfam release 23.
The top part shows the histogram of average log probability per predicted transmembrane helix; the bottom part shows the same per predicted signal peptide. The log probability provided on the x-axis is calculated with equations 5 and 6. At the TMcutoff of ≥−12 (false-positive rate 4.67%) and SPcutoff of ≥−1 (false-positive rate 4.02%), the number of predicted TM helices and signal peptides are 3849 and 164 respectively.