When interpreting the output from SignalP, you should be aware of the
- 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
- 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
- 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.
Last change: December 4, 1996,