I'm not sure if this could help you, but I just released a program that might be of use. It's primarily designed to identify places where your protein differs from the consensus, so you can mutate it to increase the stability. But it also gives you outputs of an overall consensus sequence, and a spreadsheet of amino acid frequencies across the whole length of the protein. You can at least use that to tell you what parts of your protein are highly conserved, and see if any of those regions match the binding motif.
You can try it out at http://kazlab.umn.edu/
You can try it out at http://kazlab.umn.edu/
On Thu, Jun 2, 2016 at 3:12 PM Hiro Protagonist <smeik187@gmail.com> 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
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/fa0ae295-eb5f-475f-ae37-e6866eee0eca%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CAKw3Q72Nb3pqhxZaGPTDObSNcZ1qpBj-p0Dgk%3DHsomBW339NpQ%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.
0 comments:
Post a Comment