[BiO BB] An interesting Domain occurrence?

Adarsh Ramakumar adarshramakumar at yahoo.co.uk
Sun Jan 16 05:13:28 EST 2005

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 

ALL-NEW Yahoo! Messenger - all new features - even more fun! http://uk.messenger.yahoo.com

More information about the BBB mailing list