SignalP V1.1 World Wide Web Prediction Server Center for Biological Sequence Analysis

Results: Identification of signal anchors

Above is shown the distribution of the mean S-score for three different protein types: Signal peptides, Non-secretory proteins (the N-terminal parts of cytoplasmic or nuclear proteins), and Signal anchors (the N-terminal parts of type II membrane proteins). Only eukaryotic data are shown here.

Signal anchors are also referred to as uncleaved signal peptides. However, they often have sites similar to signal peptide cleavage sites after their hydrophobic (transmembrane) region. Therefore, a prediction method can easily be expected to mistake signal anchors for peptides.

The mean S-score for signal anchors shows some overlap with the signal peptide distribution (50% of the eukaryotic signal anchor sequences have mean S-scores larger than 0.5). However, signal anchors are generally significantly longer than signal peptides. By excluding signal peptides longer than 35 residues (and using a slightly larger cutoff), 72% of the eukaryotic signal anchor sequences are correctly classified. (Only 2.2% of the cleaved eukaryotic signal peptides in our data set are longer than 35 residues).