SQUARE - Protein Design Group

SQUARE Protein Design Group

Reliability Scores (those residues that are reliably aligned are marked with an '@')

     Target   --TKYFRIPAMC--TTSKGTIVVFADARHNTASDQSFI---DTAAARSTD
              ---@@@@@@@@-----@@@@@@@@@@@@@@-----------@@@@@@@@@
     Template IFRGPDRIPSIVASSVTPGVVTAFAEKRVGGGDPGALSNTNDIITRTSRD

In this case a small rearrangement of the target residues produces much higher scoring alignment. 32 of 50 residues are classified as reliable (there were only 17 in the alignment returned by the server). By aligning "RI" of the target to "RI" of the template (instead of the FR vs FR of the first alignment) the first site residue is now aligned with an identical residue instead of a gap, and it is surrounded by other high-scoring residues (a necessity if the alignment at the site is to be reliable).

A shift around a gap at the C-terminal end of this section has also drastically improved the alignment at this end. The third site does not score too highly and the residue is not identical, but the swap (S for D) is fairly conservative and there is an aspartate next door in the target that may turn out to be in the identical position to the site residue in a structural alignment.

Residues where there is little evolutionary information in the PSSM are marked with a 'U'

     Target   --TKYFRIPAMC--TTSKGTIVVFADARHNTASDQSFI---DTAAARSTD
              --------------------------------------------------
     Template IFRGPDRIPSIVASSVTPGVVTAFAEKRVGGGDPGALSNTNDIITRTSRD

Template secondary structure (DSSP)

     Target   --TKYFRIPAMC--TTSKGTIVVFADARHNTASDQSFI---DTAAARSTD
              EE-TT-EEEEEEE-TTTTT-EEEEEEEEET-SSTT-TT-EEEEEEEEETT
     Template IFRGPDRIPSIVASSVTPGVVTAFAEKRVGGGDPGALSNTNDIITRTSRD

PDB binding sites are marked with an 'S'

     Target   --TKYFRIPAMC--TTSKGTIVVFADARHNTASDQSFI---DTAAARSTD
              ------S--------------------S----S-----------------
     Template IFRGPDRIPSIVASSVTPGVVTAFAEKRVGGGDPGALSNTNDIITRTSRD

Return to SQUARE