Signal Peptide Predictors predict Signal sequence parts and Signal
cutting sites either for Prokaryotic or for Eukaryotic species, according
to the selected method of prediction. A Signal Peptide is a specific
N-terminal sequence region with structural and physicochemical properties
that permits protein membrane anchoring, insertion and translocation,
most likely mediated by recognition mechanisms.
The class has four predictors, three for Prokaryots and only one is
Eukaryots. This is due both to their different speed of evolutionary
divergence and to the different number of representatives: Prokaryots
grow and evolve rapidly so their Domain is wider and also more diverse
in terms of species. than that of the Eukaryots. i The three Prokaryotic
class are specific for Gram Positive, for Gram Negative and for the
Gram Negative Escherichia Coli. Gram Positive and Gram Negative differs
widely in their membrane structure and chemical composition, leading to
detectable difference in their Signal Peptides. The Escherichia Coli
predictor must be considered more a refinement of the Gram Negative
class of prediction than a new predictor. This refinement is due to
the biological importance of this organism and to the wide knowledge
of its protein ensemble.
All of them are Neural Network-based. There are two Neural Networks
(NN), one dedicated to the Signal prediction and the other to the
Cutting site prediction. The NN for the Signal has a one-state output,
representing, for each residue, the likelihood to belong to a Signal.
In the table, the results for the segments are labelled
accordingly to their predicted feature:
- Target: A Signal Peptide detection is considered valid only when
both a Signal and a Cutting Site are found. The simple
detection of the Signal without its corresponding cutting
site, is not sufficient at all and will never bring to
an effective predicted Signal Peptide.
- Output: The Output is presented graphically in two colors, according to the
legend at the bottom of the image, one color each for the
predicted Signal Peptide and for the Mature Protein (the
protein, as it is after the Signal Peptide cutting process).
The Signal likelihood is also plotted as a continuous line
interpolating each discrete positional value.
Just on the top of the first image, the description line could
contain additional information indicating the detection of
a prokaryotic lipoprotein. This kind of proteins have special
cutting sites, and special aminioacidic patterns around them,
that permit lipo-anchoring.
- Signal - for the Signal Peptide
- Mature - for the rest of the Protein
For further information see:
Nielsen H., Engelbrecht J., Brunak S. and von Heijne G.;
Protein Engineering 10, (1997), 1-6.