[BiO BB] Most common protein fold?

[dmb at mrc-dunn.cam.ac.uk]

> 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.

Use the SUPERFAMILY database,

http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/

That gives you exactly what you need broken down by organism :)


> 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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