[BiO BB] protein identity

[nabula easter]

Hi Philipp, 
 many thanks for your mail. this is not a hypothetical
question. Many times i confront this type of situation
where in my BLAST report one hit is 99% identical and
when i look carefully, i find replacement of some
residues not by a similar residue but by  a totally
different residue. However, as these hits( proteins)
are hypothetical, its difficult to assess this
difference is in some functional site or presumably a
key domain ( putative) of this protein. 
  I am dealing with cDNA sequences, i i BLAST the ORF
of these cDNAs. So when i do BLASTN with cDNA , i see
these two DNA sequences are 94% identical. So its
difficult to say that these two cDNAs are identical.
I hope now my problem is clear, please suggest more .
In my analysis , i consider these sometimes as
homologs, because i see a different UNIGENE patter for
these two sequences. 
Cheers
Thrio

__________________________________________________
Do You Yahoo!?
Make a great connection at Yahoo! Personals.
http://personals.yahoo.com