Nucleic Acids Research, 2012, Vol. 40, Web Server issue W217 Figure 3. ProBiS output page for query protein (PDB/Chain ID: 2q4u.A) of unknown function. (A) Structurally conserved binding sites. (B) An interactive table of similar proteins, ﬁltered to show only calcium binding proteins. (C) Local structural superimposition of the blue query (2q4u.A) and the violet similar protein (2ehb.A) that contains a co-crystallized Ca2+ ion shown as green sphere. (D) The alignments presented as tables of residue-residue correspondences. (E) Integrated search tool. (F) Columns reordering tool. proteins in the interactive table are ranked by the standard Z-scores; Z-Scores >2.0 are colored green and those between 1.0 and 2.0 are yellow. The table can be down- loaded in a CSV format, and thus directly exported to a spreadsheet program, such as Excel. Local structural superimposition of a query protein, 2q4u.A in blue, and a similar protein 2ehb.A in violet, is shown in Figure 3C. The calcium ion was co-crystallized in 2ehb.A. Alignments of 2q4u.A with 2ehb.A are also shown in tables of residue-residue correspondences in panel D; the alignment 1 is that seen in panel C. Where available (31), the PDB, Pfam, SCOP and UniProt acces- sion numbers are at the top, and are links to external databases for structural and functional protein annota- tion. Below, the pairwise local alignments are presented in tabular form, ranked according to their Z-Scores. A continuous green dash connecting a pair of aligned residues indicates a good structural correspondence; an interrupted green dash indicates a poorer correspondence between the residues. The ‘Download’ buttons allow downloading the alignment in various formats, and the ‘View in Jmol’ button loads the alignment as shown in Figure 3C. Alignment scores for each pairwise alignment are shown in a yellow box, and are explained in detail in references (26,27). Filtering of the table by different search conditions is accomplished by the integrated search tool, shown in panel E. Here, the table was ﬁltered, so that the protein names in ‘Name’ column must contain a ‘Ca’ keyword, which ﬁlters out all but calcium-related proteins. The table columns can also be reordered, shown or hidden, using the ‘Reorder Columns’ tool in panel F.