PMAP

[Vinay Ramabhadran]

Hi Kutbuddin,
I am a graduate student from Dartmouth College. Your PMAP database
looks great and you have done a great job putting it together. I had
a few questions about it.
I work on a protein called Inverted Formin-2( INF2) ID#21926 <http://
substrate.burnham.org/lookup/cutdb/21926>. According to your database
it seems to have a caspase cleavage site. I have looked at other
caspase site predictors and those seems to show a lot more possible
cleavage sites. I wanted to know the following:
1) How did you narrow down on the potential site?
2) You have given Mass Spec as the method of identification. Is there
any other information about the cleavage?
3) Do you have an idea about which caspase might be cleaving it?

I hope you do not mind answering these question. They would be very
useful for my research.
Thanks
Vinay

[ksd]

The cut site came from CutDB.burnham.org
The link is http://cutdb.burnham.org/relation/show/21926

On the bottom of the page is the original citation for this record.
http://www.ncbi.nlm.nih.gov/pubmed/18722006?dopt=Abstract

That paper describes a global approach to identifying apoptosis
related (caspase) cleavage sites by mass spec.

You can see our annotator ("SG") made this entry based on that
publication. Click on the link in "Comments and others" on the very
bottom of the CutDB page.

In many cases of the enzyme causing the cleavage cannot be tracked
experimentally, but can be inferred based on the biology and the cut
site profile. In this case, I have not looked up the detail, but
perhaps they are able show that it must be a caspase, but cannot track
it down to a single protein.

If you know more detail, please register on CutDB and create/modify
entries.
http://cutdb.burnham.org/login/login