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Joseph A White whitejo at PILOT.MSU.EDU
Fri Sep 6 11:29:50 EST 1996

In regard to the distinction between similarity and homology, the question
I asked was not whether two very similar genes from different
organisms are homologous, but whether they are orthologous or paralogous.
Given that convergent protein structures rarely have highly similar
sequences, strong amino acid sequence similarity is a strong indicator
of homology.

The reason I posed the question is this: every week a message is posted
to this newsgroup describing newly cloned and sequenced arabidopsis
gene or cDNA sequences.  Some of these are of unknown function, and
some are described as having a particular function based on sequence
similarity, e.g. the 8/31/96 post includes

> ATMIXTA     X99809     1252bp    RNA      PLN      28-AUG-1996
>     A.thaliana mRNA for Mixta protein.
>     mixta gene; myb homologue; transcription factor; mixta.

Is genetic or biochemical function being inferred from sequence
similarity alone?  Are these orthologous or paralogous gene sequences?
Do they activate similar genes in the different organisms, arabidopsis vs.

It seems to me that we think of orthologous genes and their proteins as
being functionally equivalent, i.e. performing the same biochemical
function in the same subcellular compartment.  Paralogous genes and their
proteins then would likely perform a similar function in a different
compartment or at a different time in development.  As David Baum has
pointed out, homology can be thought of as relative to the evolutionary
time frame, so at some point in time there should be a common ancestor.
But if the genes are paralogous, they may have evolved to perform
different functions.

Joe White

(whitejo at pilot.msu.edu)
301 Biochemistry
Michigan State University
East Lansing, MI  48824

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