I have some motif enrichment data from a phosphoproteomic data set. I was wondering if there is a way to find which kinases or kinase families are associated with the motifs identified.
Hi Catherine there a number of motif databases floating around - some are listed here: https://molbiol-tools.ca/Motifs.htm
However if you have a protein that you suspect is a kinase then there are several motifs that are present in the vast majority of kinases that you can quickly look for.
For example there will be a motif associated with ATP binding towards the N-terminus (GxGxxG). There will also be the two motifs that border the t-loop (aka "activtion loop" which is generally an a-helix that converts to a b-sheet when the kinase is activated). These are DFG.......APE.
The number of amino acids between these two motifs is variable but generally ~20-30 or so (present around the "middle" of the protein). There will of course be numerous phosphorylation sites floating around (often one between the DFG/APE motifs involved in activation and one or more towards the C-terminus).
It has been a loooooooooooong time since I worked on kinases but they are several classification methods and these are generally on the basis of the nature of the extra-cellular domain motifs (i.e. ig-like loops etc).
And of course you could always blast search and then (if your protein is unknown) model it's structure using a program such as RasMol
http://www.openrasmol.org/
I hope this helps!
Gary
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