[modeller_usage] Regarding Optimal Alignment

[Ashish Runthala <ashishr AT bits-pilani.ac.in>]

Dear Modellers,
Check out this alignment
 3KIJA>------FLKPKINSFYAFEVKDAKGRTVSLEKYKGKVSLVVNVASDCQLT*
 2P31A>------------QDFYDFKAVNIRGKLVSLEKYRGSVSLVVNVASECGFT*
 2GS3A>TENLYFQSMRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQGGKT*
 2OBIA>------DDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQCGKT*
TARGET>---ENLYFQSMINSFYAFEVKDAKGRTVSLEKYKGKVSLVVNVASDCQLT*
     (I have given a space initially so that you can easily understand the alignment)

Will somebody guide me how to incorporate the distant conserved chunk ENLYFQSM from "2GS3A" template without making the shifted alignments just to satisfy this constraint. 
Is there any way to use the chunk from it along with the other conserved aligned motifs.

I know Sir Benn will definitely answer my query.

Thanks
Ashish


Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA