More Than 1,001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology
Figure 3
Average log probability plot of transmembrane helix and signal peptide predictions per domain.
The top part shows the average log probability per predicted transmembrane helix calculated per domain; the bottom part shows the same per predicted signal peptide. Whereas the y-axis shows the log probability in accordance with equation 6 applied over all predicted segments for a given domain, the x-axis represents their cumulative length. At the TMcutoff of ≥−12 and SPcutoff of ≥−1 (horizontal dashed lines), the number of problematic TM and SP domains are 1079 and 164 respectively. The total number of problematic domains is 1214 (1050 TM, 135 SP and 29 concurrent TM and SP).