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Analyze Binding Sites Dialog Box |
Calculate sequence identity in multiple alignment columns that are within a certain spatial distance from ligand residues, and filter the alignment sequences based on the sequence identity.
To open the Analyze Binding Sites dialog box, you can:
Choose Tools → Analyze Binding Site in the Multiple Sequence Viewer panel.
To analyze a binding site, you must have a sequence and a structure for the query, and the structure must have at least one ligand (it can have more). Next, you must have a set of sequences that are aligned to the query, which you can obtain from a BLAST search followed by an alignment. If you want to do the analysis for sequences other than the query, you must have structures with ligands for those sequences.
When you open the dialog box, the query sequence is analyzed and annotated with ligand contacts (for all ligands), and the columns for the residues that are in contact with the ligand (or first ligand) are selected. Sequences that have 100% identity with the query residues that are in contact with the ligand (or the first ligand) are also selected by default.
The dialog box opens at the Conservation Analysis tab. If you want to select and remove sequences that are similar to the query or different from the query in the active site, you can use the tools in this tab.
The Distance Analysis tab is useful for examining the average conservation within a set of sequences. The analysis could be repeated for different queries to obtain a comparison of the average conservation for the queries.
You can change the sequence and select the ligand with the Sequence and Ligand option menus. When you change the sequence, the new sequence is analyzed and annotated and the column selection updated for the new ligand. Changing the ligand updates the column selection.
Choose the sequence from this option menu. The analysis is done on the basis of the chosen sequence. This means that the sequence you choose must have an associated structure with a ligand.
Choose the ligand for the sequence from this option menu, if the structure for the sequence has more than one ligand. The column selection changes to represent contact with the chosen ligand.
In this tab you can select sequences based on the degree of conservation of residues in the active site (i.e. residues that are in contact with the ligand).
Use this slider to adjust the percentage sequence identity threshold for selecting sequences in the Multiple Sequence Viewer panel. As you change the value, the selection is updated to reflect the new threshold. The default is 100%, so only sequences that are completely identical for the active site residues are selected by default.
For the current threshold, remove sequences from the Multiple Sequence Viewer panel whose sequence identity in the active site is greater than the threshold. This is useful if you are looking for mutations in the active site and want to eliminate sequences that are the same or very similar in the active site.
For the current threshold, remove sequences from the Multiple Sequence Viewer panel whose sequence identity in the active site is smaller than the threshold. This is useful if you are looking for sequences that are the same or very similar in the active site, but may diverge elsewhere.
In this tab you can analyze the average identity, similarity, and homology of the residues in the alignment to the query residues that are within a range of distances of the ligand.
This table reports the results of the analysis. Each row represents a neighborhood of the selected residues. The first column is the distance cutoff for that neighborhood: any residue that has a heavy atom within that distance of a heavy atom in the selection is considered to be in that neighborhood. The remaining columns contain the identity, similarity and homology values calculated for the columns within the alignment that include the residues within the distance threshold.
Specify the range of distances over which the analysis is performed.
Export the table data to a CSV file. Opens a file selector, in which you can navigate to a location and name the file.
Analyze the residues in the alignment for their identity, similarity, and homology to the query residues that are within the specified distance threshold of the ligand.
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