One way would be to purify the kinase and the potential target protein, mix them together with MgATP, and see whether the target protein becomes phosphorylated. This could be checked by using gamma-phosphate radiolabeled ATP followed by SDS-PAGE and autoradiography, or by mass spectrometry.

If there is a known consensus sequence for phosphorylation by SNF1-like kinase, you can check the target protein to see if it has such a sequence. That would not be a guarantee, of course, since the consensus sequence in the target protein may not be accessible.

You could try knocking out SNF1-like kinase in cells and testing whether this has any effect on the phosphorylation state of the target protein, using pulse labeling and immunoprecipitation. The effect, if any, might be indirect, of course.

I worked similar sometime back in checking phosphorylation of a protein by a kinase. I think there are phosphate specific antibodies available that bind to phosphate groups. So, probably you can use Western Blot to check that. For more clarification, you can contact Prof. W. Todd Miller at Stony Brook University, NY ([email protected])

Anti-phosphotyrosine antibodies are available that will bind to any phosphotyrosine residues in a Western blot. Anti-phosphoserine or -phosphothreonine antibodies are always sequence-specific, so they would have to be raised against a phosphorylated peptide from the target protein.

If you want to check the change in overall phosphorylation patter of protein  ( Arabidopsis, yeast or human), 2-D gel electrophoresis (2-DE) is the best option. Even if you want to check the phosphorylation of selected proteins you can use 2DE. First you incubate your kinase and the potential target protein for phosphorylation. Then mix this with the purified target protein, focus this mix on IPG strip, run a 2D gel and  western blot it for  the target protein. If your protein is getting phosphorylated, you will find a shift in the protein spot ( two or more  spots, one unphosphorylated and others phosphorylated) which generally correspond to the number of phosphorylation in your protein. It is also possible to elute the spot and analyse it on LCMS/MS to identify the site of phosphorylation.

In case you want to check the overall change in phosphorylation pattern, incubate your kinase with the total protein from the desired source, focus it on IPG strip, run a 2D gel and stain it with ProQ diamond. It is a fluorescent stain which label only phosphorylated protein only. comparison with the control 2DE gel  can quantitate the total number of protein phosphorylated by your kinase, using LCMS/MS the protein and the site of phosphorylation can be identified.

Not sure if this is relevant information to you but since you mention human proteins, there is a commercial antibody designed to detect phospho-serine within a AMPK consensus site. Reference 5759 from cell signaling.