SQUARE                                    Protein Design Group


Interpretation of the scores

Profile-derived Scores for the Alignment (negative scores are irrelevant and not shown)




Reliability Scores (those residues that are reliably aligned are marked with an '@')
     Target   KSVVFKAEGEHFTD-------QKGNTIVGSGSGGTT--------------
              --------------------------------------------------
     Template PSASFYFDGKLIRDNIQPTASKQNMIVWGNGSSNTDGVAAYRDIKFEIQG

Apart from one small island of high-scoring residues (GNGSS) this first portion of the alignment scores badly. Are these 5 residues significant?


Residues where there is little evolutionary information in the PSSM are marked with a 'U'
     Target   KSVVFKAEGEHFTD-------QKGNTIVGSGSGGTT--------------
              UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU---------------
     Template PSASFYFDGKLIRDNIQPTASKQNMIVWGNGSSNTDGVAAYRDIKFEIQG

Well, no, they aren't. the first 30 or so residues in the template have very little information in their PSI-BLAST profile. This means that any scores at this point cannot be trusted. Generally the only residues that will score well are identical residues, hence the peak (GNGSS vs. GSGSG).


Template secondary structure (DSSP)
     Target   KSVVFKAEGEHFTD-------QKGNTIVGSGSGGTT--------------
              -EEEEEETTEEEEE----EE----EEEEEE--SSS-EEEEEEEEEEEES-
     Template PSASFYFDGKLIRDNIQPTASKQNMIVWGNGSSNTDGVAAYRDIKFEIQG

PDB binding sites are marked with an 'S'
     Target   KSVVFKAEGEHFTD-------QKGNTIVGSGSGGTT--------------
              --------------------------------------------------
     Template PSASFYFDGKLIRDNIQPTASKQNMIVWGNGSSNTDGVAAYRDIKFEIQG






Profile-derived Scores for the Alignment (negative scores are irrelevant and not shown)




Reliability Scores (those residues that are reliably aligned are marked with an '@')
     Target   -KYFRIP------AMCTTSKGTIVVFADARHNTASDQSFIDT---AAARS
              ------------------@@@@@@@@@@@@@@---------------@@@
     Template DVIFRGPDRIPSIVASSVTPGVVTAFAEKRVGGGDPGALSNTNDIITRTS

Residues where there is little evolutionary information in the PSSM are marked with a 'U'
     Target   -KYFRIP------AMCTTSKGTIVVFADARHNTASDQSFIDT---AAARS
              --------------------------------------------------
     Template DVIFRGPDRIPSIVASSVTPGVVTAFAEKRVGGGDPGALSNTNDIITRTS

Template secondary structure (DSSP)
     Target   -KYFRIP------AMCTTSKGTIVVFADARHNTASDQSFIDT---AAARS
              EEEE-TT-EEEEEEE-TTTTT-EEEEEEEEET-SSTT-TT-EEEEEEEEE
     Template DVIFRGPDRIPSIVASSVTPGVVTAFAEKRVGGGDPGALSNTNDIITRTS

PDB binding sites are marked with an 'S'
     Target   -KYFRIP------AMCTTSKGTIVVFADARHNTASDQSFIDT---AAARS
              --------S--------------------S----S---------------
     Template DVIFRGPDRIPSIVASSVTPGVVTAFAEKRVGGGDPGALSNTNDIITRTS

Here the alignment is almost certainly incorrect in places. Although there is a largish section in the middle and a smaller one at the C-terminal end that are reliably aligned, there are also large runs of low-scoring residues. If this were the correct template structure and correct alignment, then the query sequence will have lost almost all of the function of the template - only one of three site residues is identical in the target and one is aligned with a gap. Fortunately there is a better alignment of this section here.

The second site (in EKRVG) in this section is almost certainly aligned correctly.






Profile-derived Scores for the Alignment (negative scores are irrelevant and not shown)




Reliability Scores (those residues that are reliably aligned are marked with an '@')
     Target   TDGGKTWNKKIAIYNDRVNSKLSRVMDPTCIVA
              @@@@@@@@@@@@@@@@@@@----@@@@@-----
     Template RDGGITWDTELNLTEQINVSDEFDFSDPRPIYD

The C-terminal section is almost certainly aligned correctly. The single site residue in this section coincides with a peak score, so is reliably aligned.


Residues where there is little evolutionary information in the PSSM are marked with a 'U'
     Target   TDGGKTWNKKIAIYNDRVNSKLSRVMDPTCIVA
              ---------------------------------
     Template RDGGITWDTELNLTEQINVSDEFDFSDPRPIYD

Template secondary structure (DSSP)
     Target   TDGGKTWNKKIAIYNDRVNSKLSRVMDPTCIVA
              TTSSSS----EESSTTT-SSS-EEEEEEEEEEE
     Template RDGGITWDTELNLTEQINVSDEFDFSDPRPIYD

PDB binding sites are marked with an 'S'
     Target   TDGGKTWNKKIAIYNDRVNSKLSRVMDPTCIVA
              --------------------------S------
     Template RDGGITWDTELNLTEQINVSDEFDFSDPRPIYD




Return to SQUARE