>In article AA14252 at mailgate.eur.nl, themmen at endov.fgg.EUR.NL (themmen) writes (in part):
>> the RNA level the percentage identity (80%) is higher than the percentage
>> of identical amino acids (72%). My conviction has been that it should be
>> the other way around because of the possibility of the third base in the
>> codon to be at least two-fold redundant.
>>>> Can somebody give us an idea?
>>galtier at acnuc.univ-lyon1.fr (Nicolas Galtier) wrote accurately in reply.
However, since I have had to explain this before to others
(including my department head), I would like to offer what may be easier to grasp.
Imagine a mRNA coding for a polypeptide.
Now change the nucleotides in the third position of every codon.
You now have a nucleic acid that is 67% identical, but a polypeptide that has very few identities. That is consistent with most people's expectations.
Now starting with the same mRNA, change the nucleotides in the first position of every codon. The nucleic acids are 67% identical but the polypeptides are virtually non-identical.
So, results like those mentioned are theoretically possible.
They are actually observed not infrequently.
>What about the G+C content in third positions of the gene? It may be extreme
>in both sequences, so that percentage identity in third positions HAS to be
>high. For example, in such cases, nearly all glutamate codons are GAG rather
>than GAA in both sequences.
>G+C content in third position in vertebrates depends on the location of the
>gene on the chromosome : there are GC-rich and GC-poor regions, named
>isochores. For revue, see works of Bernardi and Mouchiroud.
>>Further, the indices you use as measures of variability are not clearly
>relevant. For one aminoacid change, I expect few more than one nucleic
>change in the corresponding codon (usually one, rarely two), so that
>percentage of differences in the nucleic _non synonymous_ positions
>(roughly positions 1 and 2) is expected to be about half the proteic one,
>as there are roughly two nucleic non-synonymous positions for each
>aminoacid position. To compare proteic and nucleotidic divergences,
>you cannot avoid separating synonymous and non-synonymous sites.
Ulrich Melcher umelcher at bmb-fs1.biochem.okstate.edu
Department of Biochemistry
and Molecular Biology Tel: 405-744-6210
246 NRC FAX: 405-744-7799
Oklahoma State University
Stillwater OK 74078-3035 USA