[BiO BB] Most common protein fold?

Boris Steipe boris.steipe at utoronto.ca
Thu Oct 6 08:48:10 EDT 2005


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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