Use the output from the substrate prediction program as a guide for designing input for Scansite Quick Matrix Method phosphorylation site prediction.

Example suggestions for filling in Scansite primary and secondary preferences are listed in the table below.
Primary
Secondary

(-3)
R/K
Q

(-2)
Hydrophilic

Hydrophobic
S/T

T/P/A/G

(-1)
X
X

(+1)
P

F/I/L/M

V/I/L/M
leave blank (no X)

V

C

(+2)
Hydrophilic

Hydrophobic
S/T

V/A/P

(+3)
F/L/K/R
S/T/A/G

Go to Scansite Quick Matrix Method

 

 

After making a submission to Scansite Quick Matrix Method

  • Enter a species name.
  • Check either SwissProt or TrEMBL. TrEMBL contains newer, uncharacterised or theoretical proteins.
  • Enter keywords from SwissProt protein name field (if known) such as checkpoint.
  • Enter no more than 300 for the number of hits.
  • For a single protein search, in the "sequence contains" box, enter a fragment of unique sequence from the protein. It does not have to contain the phosphorylation site.
  • Hits will be in scoring order. Hits from a single protein may be in sequence order.

Also see examples of predictions made with the program.