Help! Amino acid homology <50%

[Brian Foley]

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                         |
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