Help! Amino acid homology <50%

[Mary P. Remington]

How significant is a homology at the amino acid level (between different
species) of less than 50%?  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.  

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