Protein domain database?

[Suresh Kumar]

Hi Ed,

Here is the information that you are looking for.

http://www.uniprot.org/uniprot/P22607

Scroll down to the Sequence annotation section and you will find the answer. The sequence information is given as "potential" probably based on the prediction algorithm.
You may still want to check the original reference to verify it.

This information is also available through NCBI protein search. 
But you need to look harder. :)

-Suresh



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Subject: Methods Digest, Vol 43, Issue 9

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Today's Topics:

   1. Re: Size-Exclusion (WS)
   2. Protein domain database? (Ed Siefker)


----------------------------------------------------------------------

Message: 1
Date: Wed, 10 Dec 2008 14:15:40 -0800 (PST)
From: WS <novalidaddress from nurfuerspam.de>
Subject: Re: Size-Exclusion
To: methods from net.bio.net
Message-ID:
	<d6009bc3-d305-4614-b9cf-1b84b6f0ee9f from y1g2000pra.googlegroups.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Jan.

Actually, NaCl (as all small ions) should distribute evenly across the
column when it has been equilibrated. Can you perform online
conductivity monitoring? - You should be able to "see" the constant
salt concentration in the solvent.
Another issue might be that your protein becomes too concentrated and
then precipitates and/or denatures. In that case, try to work at a
higher dilution or -if appropriate- try to optimize salt
concentration, pH or add eg urea (maybe also sucrose or maltose will
do, try to use something that does not disturb your activity assay) in
order to stabilize your enzyme.

Best reagrds,

Wolfgang

On Dec 10, 11:50 am, "Jan R. Krähling" <J-R.Kraehl... from tu-
braunschweig.de> wrote:
> Hello!
>
> We are trying to establish the sixe-exclusion chromatography in our lab to purify the enzyme of our interest. In the purification-steps before the  size exclusion we observe that a NaCl-concentration of 1M stabilize the enzyme better than lower NaCl concentrations. So we tried the size exclusion at first with a high salt concentration, but the enzyme wasn't detectable. At lower concentrations the enzyme is detectable and active. My question is, if it is possible, that through the size-exclusion the salt-concentration increased to such a high level, that this will damage the enzyme. Is it possible that the elution of NaCl is so strong delayed, that at the top of the column unexpected high concentration of NaCl occur?
>
> Thanks for your help!
>
> Jan


------------------------------

Message: 2
Date: Wed, 10 Dec 2008 17:06:37 -0600
From: Ed Siefker <ebs15242 from creighton.edu>
Subject: Protein domain database?
To: methods from magpie.bio.indiana.edu
Message-ID: <49404B7D.6060502 from creighton.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

I am trying to answer what should be a simple question.
That is, which residues of FGFR3 are intracellular?

I'm shocked to find that this information isn't in any
of the usual databases.  NCBI's gene page for FGFR3 doesn't
have it.  If I click through to the protein sequence, it's
not marked as a feature.  The RCSB protein data bank doesn't
seem to have this information either.

Now obviously I can search the literature and find a reference
that has this information. I'll be doing that tomorrow. But
isn't this the kind of thing we should be able to find out with
a few clicks in a database? Is there a database that has this
kind of information, and I'm just not finding it?  If not, why not?
-Ed



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