Help! Amino acid homology <50%
btf at lanl.gov
Thu Apr 1 13:28:58 EST 1999
Mary P. Remington wrote:
> How significant is a homology at the amino acid level (between different
> species) of less than 50%?
Are you asking about 50% amino acid identity (where
only identical amino acids contribute to the score)? Or 50%
similarity (in which similar amino acids such as Lue and Ile
contribute to the score)?
In either case, 50% is above the random expectation,
so the sequences can be considered to be related in some
fashion, perhaps by sharing a common ancestor.
> I have PCR-ed a gene from a cDNA using the 5'
> and 3' sequence from a sequence in Genbank. The fragment I amplified
> bears no resemblence to the Genbank sequence. The Genbank sequence in
> question when translated is less than 50% homologous to the same gene from
> different species. There is a much higher degree of homology between the
> other species than the one species I am trying to amplify.
I don't undestand this part. Are you saying your sequence
is something like 70% identical to the sequence from another
species, and about 50% identical to the sequence you originally
designed primers to? What organisms are you talking about here?
> The Genbank sequence in question was generated from probing a cDNA
> library. This generated a 3' clone. The 5' end was generated by using
> the RACE protocol. So, I am wondering if there might not be a problem
> with the sequence. Any suggestions or ideas appreciated. Thanks, Mafy
Anything is possible. Is the 3' end of the GenBank
sequence 90% identical to your sequence, while the 5' end
is only 20% identical?
|Brian T. Foley btf at t10.lanl.gov |
|HIV Database (505) 665-1970 |
|Los Alamos National Lab http://hiv-web.lanl.gov/index.html |
|Los Alamos, NM 87544 U.S.A. |
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