This example from Patricia Babbitt's research group at UCSF shows an alignment of three proteins in the enolase superfamily. The Babbitt group is characterizing superfamilies of enzymes whose member proteins perform a broad range of biochemical functions while sharing a common active site architecture.
The color swatches behind the sequence names match the corresponding structures. Three residues from each protein are shown as ball-and-stick in the structure and highlighted with purple in the sequence alignment. These conserved residues bind a divalent metal ion (shown as a red ball) important for function; along with other residues (not shown), they provide the machinery for abstracting a proton alpha to a carboxylic acid. This partial reaction is the common feature of enolase superfamily members.
The red serine in the sequence dialog indicates a mismatch between the provided alignment sequence and the structure sequence, which actually has a threonine in that position.
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