[BiO BB] Most common protein fold?

[paul]

Hi Boris,

Thanks you for this, but I was really wondering how many individual known
proteins fall within each class and subclass (i.e. superfamilily, family,
etc.). For example, how many individual proteins adopt the Ribulose-phoshate
binding barrel fold and how are the proteins distributed between the four
families? In other words, I am not trying to find out how many different
clases and subclasses of protein folds we have, but rather how are known
proteins (e.g. those in Swiss-Prot or PDB for example) distributed amoungst
the various folds? Hope this makes sense?!

Best Regards,

Paul

-----Original Message-----
From: bio_bulletin_board-bounces+p.curley=wmin.ac.uk at bioinformatics.org
[mailto:bio_bulletin_board-bounces+p.curley=wmin.ac.uk at bioinformatics.or
g]On Behalf Of Boris Steipe
Sent: Thursday, October 06, 2005 5:48 AM
To: The general forum at Bioinformatics.Org
Subject: Re: [BiO BB] Most common protein fold?


The SCOP help-file at http://scop.mrc-lmb.cam.ac.uk/scop/help.html
Has the following to say:

"The number in parenthesis after an entry shows how many children
will be found there."

So for example the TIM b/a barrel Fold
----- TIM beta/alpha-barrel [51350] (31)
has 31 superfamilies and its Ribulose-phosphate binding barrel
---------- Ribulose-phoshate binding barrel [51366] (4)
has 4 families.

Hope this is what you were looking for

Boris
==========================================

On 6 Oct 2005, at 13:46, paul wrote:

> Hi Folks,
>
> Quick question. Does anyone know by any chance know how I can find the
> number of individual proteins within
> each superfamily and family of the SCOP database to get an idea of
> which
> folds are the most
> common and which are very rare?
>
> Any help much appreciated.
>
> Best Regards,
>
> Paul
>
> -----Original Message-----
> From: bio_bulletin_board-bounces
> +p.curley=wmin.ac.uk at bioinformatics.org
> [mailto:bio_bulletin_board-bounces
> +p.curley=wmin.ac.uk at bioinformatics.or
> g]On Behalf Of Boris Steipe
> Sent: Wednesday, October 05, 2005 9:57 AM
> To: The general forum at Bioinformatics.Org
> Subject: Re: [BiO BB] In search of complete conserved genes....
>
>
> This is what COGS was built for:
>
> http://www.ncbi.nlm.nih.gov/COG/
>
> "Interesting" interface though. Probably the list you might want to
> work with is
> http://www.ncbi.nlm.nih.gov/COG/old/palox.cgi
>
>
> Boris
>
>
> dwivedbz at notes.udayton.edu wrote:
>
>
>
>> Hello everyone!
>>  I am looking for complete conserved protein-coding genes that are
>> widely distributed among bacterial species (should be present in
>> atleast 6-7 bacterial species). Also, I need such genes to show
>> high degree of sequence similarities in the species they exist. I
>> would appreciate if you could help me out.  Thanks!
>>  Bhakti
>>
>> ---------------------------------------------------------------------
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