I ran a search for possible phosphorylation sites using online softwares. But how do I go ahead to predict which kinase may cause phosphorylation?
Do you have a method for purified this protein?
Mass spectrometry of a tripsinized digestion. The peptide phosphorylated would have a different m/z.
Alternatively, you can test the effect of some kinase inhibitors.
Could you try cross-linking proteins in vivo to "capture" the transient kinase-protein interaction?
Perhaps this would be of interest to you: http://link.springer.com/protocol/10.1007%2F978-1-61779-337-0_12
Then you would need some way to isolate your cross-linked complex, perhaps by immunoprecipitation if you have an antibody to your protein.
Try NetPhosK 1.0 Server, it makes prediction about kinases. Maybe it could work with prokaryotic proteins, too.
If you can purify this protein, 15N-labeled, then add the putative kinase, ATP and Mg and see by NMR 2D 1H-15N HSQC if the protein is phosphorylated and where. See about this, the last article of Selenko P:
Theillet FX, Rose HM, Liokatis S, Binolfi A, Thongwichian R, Stuiver M, Selenko P.
Nat Protoc. 2013;8(7):1416-32. doi: 10.1038/nprot.2013.083. Epub 2013 Jun 27.
Maybe you can apply it also to your prokaryotic protein.
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