[go] ISA/ISO

[Benjamin Hitz]

Val -
This is a bad example.

Orthology implies an evolutionary relationship.  If there is no  
detectable sequence similarity and no detectable structural  
similarity, I don't see there is any evidence for an evolutionary  
relationship.

I think for both Nse6 (Pombe) and presumed orthologes in other  
species - there is no known structure, hence you cannot conclude  
whether or not they have a similar (analgous?) function due to  
convergent or divergent evolution.

Ben


On Feb 21, 2008, at 5:54 AM, Valerie Wood wrote:

> In support of the final sibling arrangement of ISA/ISO, I came  
> across an example today where gene products are known to be  
> orthologous but have no sequence conservation which I thought I  
> would share.
>
> Identification of the Proteins, Including MAGEG1, That Make Up the
> Human SMC5-6 Protein Complex
> Elaine M. Taylor, Alice C. Copsey, Jessica J. R. Hudson, Susanne  
> Vidot, and Alan R. Lehmann
> quote
> "Nse6 contains ARM/HEAT repeats, but there is no sequence  
> conservation between these presumed orthologs from S. cerevisiae/  
> and /S. pombe/. In /S. pombe/ they also appear to bridge the head  
> domains of Smc5 and Smc6"
>
> where it is not even possible to detect the similarity between the  
> 2 nse6 subunits in yeast and pombe but they are presumed orthologs  
> from other biological properties and position in the complex,  
> binding partners etc.
> These are NOT reciprocal best hits, and although they can be  
> aligned, (you can align anything) it does not mean, that if I  
> inferred any  experimental data from the S. cerevisiae ortholog it  
> would come from a sequence alignment.
>
> I should also add that this is very common which also has large  
> implications for the orthology prediction exercise.
>
>
> Val
>
>
>
> -- 
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--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
Consortium
Stanford University ** hitz at genome.stanford.edu