[BiO BB] doubt in protein modeling step

[Ayyagari Kiran]

Hi all,
In protein modeling,at first we look for protein
sequence similarity and doing Multiple Seq alignment. 
Supposing I take 5 protein sequences hits (after doing
Blastp),assuming that there are no pdb structures for
any of them but still i have to model my protein
sequence. 
the next step is to go for Multiple sequence alignment
where in we can find out which are the regions exactly
conserved and find whether those regions have any
structural similarity also!!!

But here the input for Multiple Sequence alignment is
our query sequence + the 5 similar 
sequences having highest hits (from BLAST)

my question is whether we can/should build a consensus
sequence by multiple alignment taking into
consideration our query sequence also??

or build a consensus sequence by Multiple alignment
taking only those 5 sequences (excluding our query
seq) and then align that consensus sequence with our
query sequence both at sequence level and structure
level.
I shall refine my doubt if am not clear in my
subsequent discussions.Thanks in advance

Ayyagari Kiran 
 

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