[BiO BB] Most common protein fold?

Boris Steipe boris.steipe at utoronto.ca
Thu Oct 6 12:24:21 EDT 2005


Hi Paul,

In my mind it would only make sense per organism, because the number  
of "known" proteins is an arbitrary subset. Wouldn't you agree? Then  
again, I am not even sure the number of known genes in an organism is  
all that meaningful either, because they are expressed at hugely  
different levels ... is the mere presence of a gene enough to support  
the type of inference you are looking for?

For folds-per-organism it seems the SUPERFAMILY database referred to  
by "dmb at mrc-dunn.cam.ac.uk" is indeed your best bet.

Does this help?

Boris


On 6 Oct 2005, at 19:03, paul wrote:

> 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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