Organisation of ELISA. Elisa is divided into two levels. On the first level, a user needs to define a domain on the PDUG with the closest homology (blue square). This step can be done either through sequence homology, structure, function or taxonomic representation. For example, in the sequence query the closest homologue or set of homologues is identified. After a single domain of interest is placed, all information about the sequence, structure and function of that node is available. The next level asks to define a complex query that delineates all neighbors of the domain in question thus delineating the SSF neighborhood. For example, if we consider the node with a blue square, all the nodes with red squares constitute its structural neighbors at some similarity cutoff. The constraints on delineating the neighborhoods may include structure, function or taxonomic representation characteristics. ELISA then calculates consensus functional, structural and taxonomic trees for the whole SSF neighborhood defined in the previous step (not shown on picture).