[BiO BB] Most common protein fold?

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

> 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?!

Yes it does make sense. You will find a highly scale free distribution,
with many proteins being described by only a few folds, with a large
number of 'unique' folds to boot.

For example, see...

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7990952&dopt=Citation

Title:
Protein superfamilies and domain superfolds.

Abstract:
As the protein sequence and structure databases expand rapidly a better
understanding of the relationships between proteins is required. A
classification is considered that extends the sequence-based superfamilies
to include proteins with similar function and three-dimensional structures
but no sequence similarity. So far there are only nine protein folds known
to recur in proteins having neither sequence nor functional similarity.
These folds dominate the structure database, representing more than 30 per
cent of all determined structures. This observation has implications for
protein-fold recognition.



>> 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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