Re: [DIYbio] Re: protein consensus sequence recognition site prediction software

I think that I might have expressed what I am searching for in the wrong way.  I'm not searching for the sites in ATG13 but the parts in TOR which are able to bind to the sites. I found a program called COACH,  however this only shows drugs binding to it not proteins.

On 3 Jun 2016 08:21, "Jeroen Delcour" <jeroen...@gmail.com> wrote:

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:

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=YJR066W_BY4742] is a kinase which phosphorylates one of my proteins of interest - ATG13 [http://www.yeastgenome.org/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/PMC2815578/] wherein eight important sites were identfied.

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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