The 3DM system wide search by sequence helps you to identify the 3DM system for your protein.
This search first identifies the closest 3DM systems (by a HMM search) and then performs a BLAST search against the selected systems to identify the closest proteins in those 3DM Systems.
The resulting 3DM systems are shown in the system hits box, together with a domain annotation of your query sequence so that you can easily see which 3DM systems covers which domain.
By default only a selection of the top 3DM systems are shown to give a better overview.