Welcome to the 3DM walkthrough. A 3DM system is a data integration platform, we collect and integrate data about a protein superfamily.
In the case of search proteins by position motif, we're looking for specific motifs on specific positions - for example we might want to find all proteins that have a tyrosine on alignment position 35 and an isoleucine on alignment position 90, then we will use the search term "Y35,I90"
You can simplify your work with the protein of interest even more by creating a custom numbering scheme - that will cause the alignment positions to be renumbered to match the residue numbering of your protein.
If we want to analyse only some of the proteins present in the system - for example only the closest homologs of the query protein than we'll need the subsets functionality. We're going to create a subset of 100 closest proteins to our P10275 protein. To do that we need to again go to the protein detail page P10275 and click in the sequence tab.