[BiO BB] An interesting Domain occurrence?

[Howard Oliver]

please remove me - thanks

Howard Oliver
Partner, What If What Next (TM)
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-----Original Message-----
From: bio_bulletin_board-bounces at bioinformatics.org
[mailto:bio_bulletin_board-bounces at bioinformatics.org]On Behalf Of
Stefanie Lager
Sent: Monday, January 17, 2005 1:26 AM
To: bio_bulletin_board at bioinformatics.org
Subject: Re: [BiO BB] An interesting Domain occurrence?


Maybe you also could take a look at the Panther HMM database
https://panther.appliedbiosystems.com/ . It's released freely now (can
be downloaded also) and they use phylogeny when they construct the
families. Panther will also be included in Interpro soon
http://www.ebi.ac.uk/interpro/release_notes.html

Stefanie


> Hello All,
> Is there any where a list of typical domains that
> exist only in eukaryotes against which I can screen my
> prokaryotic proteins. The reason for such a question
> is; I have come across a few proteins in the genome(I
> am working with) that have Znf_NFX( Znf_NFX1,PF01422)
> and it looks more to me like a eukaryotic domain
> (based on Interpro taxon distribution, and also from
> Pfam species tree).I have screened a few (selective
> 40) bacterial genomes & I haven't come across its
> presence either. How ever just like to mention that
> Interpro could be wrong as I do know of a protein in
> one more bacterial genome which has this. So now I am
> very curious to see and cross validate if more such
> cases happen to be present. I would appreciate any
> input in this regard.
> 
> The cynic in me is curious to know if just the
> occurrence of 6-7 genes with Znf_NFX domains,means
> anything much, assuming that this domain is strictly
> non prokaryotic. Further to make it interesting the
> closest genome relative sharing 96% at 16s level
> doesn't have even a single copy of this domain, Am i
> embarking in to something interesting?
> 
> One may rise the question if these proteins are even
> expressed and real(not pseudogenes).The lab
> experiments are clear that these proteins are
> expressed. The domain have been checked for alignment
> and they are good as well.
> 
> Secondly there are many cases I know off where
> proteins sharing high level of identity(73%) and also
> annotated to have similar function but when screened
> them for domains, they do not always share the domain.
> Any explanation for this please?( except possible HGT,
> but still........)
> 
> Any set rules established on architecture of domains
> in correlation to their occurrence in proteins?
> 
> I would highly appreciate any inputs you guys can
> offer in this direction. Have a great day!
> My ears are very curious to listen to the experts.Just
> to mention I screen against SMART,Pfam,
> Prodom,Tigerfam and InterPro.
> 
> Kindest regards,
> 
> Adarsh Ramakumar
> 
> 
> 	
> 	
> 		
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