Figure 1. Structure of the protein phospholipase C, from the bacterium that causes gas gangrene. The dashed line shows the delineation of the protein into two structural domains.

Figure 2. BLAST alignment of two protein sequences.

Figure 3. BLAST result where only partial similarity is found.

Figure 4. Schematic showing the domain organization of two proteins that share similarity over part of their length: they contain a pair of CBS domains in common.

Figure 5. Multiple-sequence alignment of CBS domains. The leftmost column gives the protein identifier followed by two numbers that give the start and end positions of the domain in the whole sequence. The sequence of each domain is represented as a single row. Conserved positions are shaded to highlight potentially interesting regions of the proteins. Different shades represent the different physicochemical properties of groups of amino acids.

Figure 6. Phylogenetic tree of the PALP enzyme family proteins. The topmost sequence in the tree, labeled ‘QUERY SEQUENCE’, is the protein for which we wish to know the function. The tree has been divided into four major functional groups: group I are threonine synthases, group II are cysteine synthases, group III are tryptophan synthases and group IV are serine and threonine deaminases.