SignalP-NN result: for Humant WNT-1
# data
>Sequence
length = 70
# Measure Position Value Cutoff
max. C
30
0.565
0.32
max. Y
30
0.690
0.33
max. S
12
0.989
0.87
mean S
1-29
0.852
0.48
D
1-29
0.771
0.43
# Most likely cleavage site between
signal peptide?
YES
YES
YES
YES
YES
pos. 29 and 30: VTT-EI
SignalP-HMM result:
# data
>TXN4_HUMAN
Prediction: Signal peptide
Signal peptide probability: 0.984
Signal anchor probability: 0.015
Max cleavage site probability: 0.962 between pos. 29 and 30
# gnuplot script
for
making
Explain the output. Go back.
the
plot(s)
DESCRIPTION OF THE SCORES
The graphical output from SignalP (neural network) comprises three different scores, C, S and Y. Two additional
scores are reported in the SignalP3-NN output, namely the S-mean and the D-score, but these are only reported
as numerical values.
For each organism class in SignalP; Eukaryote, Gram-negative and Gram-positive, two different neural networks
are used, one for predicting the actual signal peptide and one for predicting the position of the signal peptidase I
(SPase I) cleavage site. The S-score for the signal peptide prediction is reported for every single amino acid
position in the submitted sequence, with high scores indicating that the corresponding amino acid is part of a
signal peptide, and low scores indicating that the amino acid is part of a mature protein.
The C-score is the ``cleavage site'' score. For each position in the submitted sequence, a C-score is reported,
which should only be significantly high at the cleavage site. Confusion is often seen with the position numbering of
the cleavage site. When a cleavage site position is referred to by a single number, the number indicates the first
residue in the mature protein, meaning that a reported cleavage site between amino acid 26-27 corresponds to
that the mature protein starts at (and include) position 27.
Y-max is a derivative of the C-score combined with the S-score resulting in a better cleavage site prediction than
the raw C-score alone. This is due to the fact that multiple high-peaking C-scores can be found in one sequence,
where only one is the true cleavage site. The cleavage site is assigned from the Y-score where the slope of the Sscore is steep and a significant C-score is found.
The S-mean is the average of the S-score, ranging from the N-terminal amino acid to the amino acid assigned
with the highest Y-max score, thus the S-mean score is calculated for the length of the predicted signal peptide.
The S-mean score was in SignalP version 2.0 used as the criteria for discrimination of secretory and nonsecretory proteins.
The D-score is introduced in SignalP version 3.0 and is a simple average of the S-mean and Y-max score. The
score shows superior discrimination performance of secretory and non-secretory proteins to that of the S-mean
score which was used in SignalP version 1 and 2.
For non-secretory proteins all the scores represented in the SignalP3-NN output should ideally be very low.
The hidden Markov model calculates the probability of whether the submitted sequence contains a signal peptide
or not. The eukaryotic HMM model also reports the probability of a signal anchor, previously named uncleaved
signal peptides. Furthermore, the cleavage site is assigned by a probability score together with scores for the nregion, h-region, and c-region of the signal peptide, if such one is found.
EXAMPLES OF STANDARD OUTPUT
By default the server produces the following output for each input sequence:
Example 1: secretory protein
The example below shows the output for thioredoxin domain containing protein 4 precursor (endoplasmic
reticulum protein ERp44), taken from the Swiss-Prot entry TXN4_HUMAN. The signal peptide prediction is
consistent with the database annotation.
>TXN4_HUMAN
Example 2: non-secretory protein
The example below shows the output for BMP-2 inducible protein kinase (EC 2.7.1.37), a nuclear protein taken
from the Swiss-Prot entry BM2K_HUMAN. No signal peptide is predicted.
>BM2K_HUMAN
SignalP-NN result:
# data
>BM2K_HUMAN
# Measure Position
max. C
20
max. Y
20
length = 70
Value Cutoff
0.035
0.32
0.034
0.33
signal peptide?
NO
NO
max. S
mean S
D
12
1-19
1-19
0.263
0.063
0.049
0.87
0.48
0.43
NO
NO
NO
SignalP-HMM result:
# data
>BM2K_HUMAN
Prediction: Non-secretory protein
Signal peptide probability: 0.157
Signal anchor probability: 0.023
Max cleavage site probability: 0.027 between pos. 28 and 29
# gnuplot script
for making the plot(s)
Explain the output. Go back.
EXAMPLE OF SHORT OUTPUT
When selecting the short output format, the prediction for each submitted sequence (in a multisequence FASTA
file) are reported on single line, one for each fasta entry. A two line header is included, showing the information of
the different columns.
# SignalP-NN euk predictions
# SignalP-HMM euk predictions
# name
Cmax pos ? Ymax pos ?
name
! Cmax pos ? Sprob ?
TXN4_HUMAN
0.565 30 Y 0.690 30 Y
TXN4_HUMAN S 0.962 30 Y 0.984 Y
BM2K_HUMAN
0.035 20 N 0.034 20 N
BM2K_HUMAN Q 0.027 29 N 0.157 N
Smax
pos ?
Smean ?
D
?
0.989
12 Y
0.852 Y
0.771 Y
0.263
12 N
0.063 N
0.049 N
#