SignalP 4.0: discriminating signal peptides from transmembrane regions

The secretory signal peptide is a ubiquitous protein-sorting signal that targets its passenger protein for translocation across the endoplasmic reticulum membrane in eukaryotes and the cytoplasmic membrane in prokaryotes1. Many methods have been published for predicting signal peptides from the amino acid sequence, including SignalP2,3,4, PrediSi5, SPEPlip6, Signal-CF7, Signal-3L8 and Signal-BLAST9. A benchmark study done in 2009 found SignalP 3.0 to be the best method10. All these methods, however, have only limited ability to distinguish between signal peptides and N-terminal transmembrane helices. Both peptides are hydrophobic, but transmembrane helices typically have longer hydrophobic regions. Also, transmembrane helices do not have cleavage sites, but the cleavage-site pattern is in itself not sufficient to distinguish the two types of sequence. This is a substantial problem because a scan for signal peptides in any complete genome will yield a lot of false positive predictions from N-terminal transmembrane regions.