target=_top
In general, conserved residues tend to be near or at known active sites. The proteins shown below were colored according to the conservation scores calculated by Jalview, which was also used to visualize the multiple sequence alignments produced by MUSCLE . But conservation is not the only indicator of an active site; in most cases the largest pocket/cavity is the active site. Images (a) and (c), rendered by PyMOL, clearly show a highly conserved region with a large pocket; they are the known active sites of FtsZ and CoaD.
FtsZ protein with surface colored by conservation score FtsZ protein with surface colored by conservation score (back)
(a) FtsZ front (b) FtsZ back
CoaD protein with surface colored by conservation score CoaD protein with surface colored by conservation score (back)
(c) CoaD front (d) CoaD back