[go] ISA/ISO

[Gwinn Giglio, Michelle]

Hi Val,

The definition of ortholog is that the two sequences arose from a common
ancestor and were separated by a speciation event.  The situation you
describe sounds to me like there is good evidence that the two proteins
carry out the same functions, however they could either be orthologs that
have diverged so much that no recognizable sequence similarity remains or
they have arisen due to convergent evolution and are NOT true orthologs.

Michelle




On 2/21/08 8:54 AM, "Valerie Wood" <val at sanger.ac.uk> 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
> 
>