Important notes

SignalP predicts secretory signal peptides

In some contexts, target peptides for chloroplasts and mitochondria or peptides involved in intracellular signal transduction are referred to as "signal peptides". These are not similar to the signal peptides predicted by SignalP, which serve as signals for entering the secretory pathway.

Prokaryotic lipoprotein cleavage sites are not predicted

Some prokaryotic lipoproteins are cleaved by a specific lipoprotein signal peptidase, Lsp or signal peptidase II. This peptidase recognizes a conserved sequence and cuts upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached. The cleavage sites of these proteins differ considerably from those cleaved by the standard prokaryotic signal peptidase (Lep).

More information about prokaryotic lipoproteins and their consensus sequence can be found in the PROSITE entry PROKAR_LIPOPROTEIN. Sequences may be scanned for the occurrence of PROSITE consensus patterns with the ScanProsite server.

Check the length of the predicted signal peptide

If SignalP predicts an abnormally short or long signal peptide, you should be aware that it might be a false prediction. You can compare with the length distribution of our signal peptide data set.

Specifically, if SignalP predicts a eukaryotic signal peptide with a length over 30 residues, it might be uncleaved. See the page about identification of signal anchors.

Include position +1 in your sequence

The C- and Y-scores are trained to be maximal at position +1 (immediately after the cleavage site). If a submitted signal peptide sequence does not include position +1, the cleavage site will be invisible. Therefore, if you want to submit a putative signal peptide alone (with none of the mature protein included), append at least one `X' to the C-terminal of your sequence.

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