The output from NetPhos contains three parts for each sequence analyzed.
The first part shows the name and length of the sequence followed by the amino acid sequence. Then follows an assignment field describing the predicted category for each residue. If the residue is predicted NOT to be phosphorylated, either because the score is below the threshold or because the residue is not Ser, Thr, or Tyr, that position is marked by a dot ('.'). Residues having a prediction score above the threshold are indicated by 'S', 'T' or 'Y', respectively.
Below the assignment line, the number of predicted S/T/Y phosphorylation sites is shown.
The second part describes the predictions for each type of residue (Ser, Thr or Tyr).
The third part is a graph illustrating the predictions (can be omitted
if the 'Generate graphics' button has been un-checked).
In the example below, T-7, S-18, Y-19, and Y-23 are predicted as potential phosphorylation sites. S-18 has a score of 0.942 indicating a very likely phosphorylation site, whereas Y-19 has a score of only 0.502. The latter score is just barely above the threshold (0.500) and indicates that the confidence for this site being a true phosphorylation site is quite low.
In general the higher the score, the higher the confidence of the prediction
and the higher the similarity to one or more of the phosphorylation sites
used in training the method.
Name: test1 Length: 26 <-- Sequence name, length QWERRRTYELVISLIVESYEAHYEAH <-- Submitted sequence ......T..........SY...Y... <-- Assignments. S,T,Y indicates predicted phosphorylation sites
Ser: 1 Thr: 1 Tyr: 2 <-- No. of predicted S,T,Y phosph. sites
Serine predictions Name Pos Context Score Pred _________________________v_________________
test1 13 ELVISLIVE 0.017 . test1 18 LIVESYEAH 0.942 *S* _________________________^_________________ Threonine predictions Name Pos Context Score Pred _________________________v_________________
test1 7 ERRRTYELV 0.921 *T* _________________________^_________________ Tyrosine predictions Name Pos Context Score Pred _________________________v_________________
test1 8 RRRTYELVI 0.056 . test1 19 IVESYEAHY 0.502 *Y* test1 23 YEAHYEAH- 0.885 *Y* _________________________^_________________
Scientific problems: Technical problems: