Uniprot is a great resource for these kind of things. Here's the page with all info about ATG13 in yeast: http://www.uniprot.org/uniprot/Q06628
Scroll down to "PTM / processing" and the "Amino acid modifications" and you'll find a list of known binding sites.
Hm, it seems all of them refer to the paper you've already found. But there's a lot of them it seems. Why do you want to find more? In my experience in-silico predictions are very unreliable, you'd still need to mutate and verify each possible site it finds anyway, which is a lot of work.
Cheers,
Jeroen
On Thursday, 2 June 2016 22:12:51 UTC+2, Hiro Protagonist wrote:
-- Scroll down to "PTM / processing" and the "Amino acid modifications" and you'll find a list of known binding sites.
Hm, it seems all of them refer to the paper you've already found. But there's a lot of them it seems. Why do you want to find more? In my experience in-silico predictions are very unreliable, you'd still need to mutate and verify each possible site it finds anyway, which is a lot of work.
Cheers,
Jeroen
On Thursday, 2 June 2016 22:12:51 UTC+2, Hiro Protagonist wrote:
Dear DIY-Biologists
I currently work on a project which aims to re-engineer TOR in S.cerevisiae BY4742 in order to lose its specifity for certain substrates.
As TOR1 [http://www.yeastgenome.org/cgi-bin/FUNGI/getSeq.pl?seq= ] is a kinase which phosphorylates one of my proteins of interest - ATG13 [http://www.yeastgenome.org/YJR066W_BY4742 cgi-bin/FUNGI/getSeq.pl?seq= ],YPR185W_BY4742
I tried to figure out which sites in ATG13 are subject to TOR dependent phosphorylation and important for inhibitition of autophagy. This lead me to the ATG13 8SA mutant[http://www.ncbi.nlm.nih.gov/pmc/articles/ ] wherein eight important sites were identfied.PMC2815578/
This again leads me to my current main problem, which is to identify where TOR is able to bind and/or identify (to) the related motif in ATG13 [S-X-S*-P].
Are there any programs available to predict these recognition sites [preferable with fasta support (not only pdb)] ?
Thanks in advance
Bruno Lederer
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