Comparison of an alignment generated by AMPS (PAM250 matrix, gap-penalty 6, tree order) and the reference structural alignment of Family 75 (Ferredoxin-like). The top block shows the AMPS alignment which contains the name of each domain, average PSE (in brackets) and the multiple alignment. The second block shows the reference multiple alignment obtained by 3D-structure comparison with STAMP . The third block shows the secondary structure as determined by DSSP  and aligned in the same way as for the reference alignment. The Structurally Conserved Regions (SCRs) as determined by the STAMP multiple structure alignment program are boxed. Symbol 'H' in the "Pij" row indicates a STAMP  P
value of 10 or higher when aligning the least similar pair of structural sub-familes in the alignment. Thus, the boxed regions show regions where the reference alignment is most reliable. Outside these regions, the proteins either do not share the same conformation, or STAMP will not label them as confidently aligned. Residues where the alignment agrees with the reference are shown with a blue background, while residues that disagree are shown with a yellow background. The Figure is produced by ALSCRIPT  from commands generated by OXBench software. See text for further discussion of this alignment.