Structure-based multiple sequence alignment (SB-MSA)

3DM uses a structure-based multiple sequence alignment to connect the proteins of a superfamily.

The alignment is divided into 'core regions', which represent the most conserved parts of the proteins in the superfamily. On the alignment page, these core regions are shown as separate, numbered alignments.

Between these core regions are 'variable regions', which differ between proteins and are not aligned. These variable regions can vary in sequence and length per protein.

The aligned core regions form the foundation of the 3DM system. Via these aligned regions, residue and alignment information can be transferred to other proteins or structures in the superfamily.

Subfamily alignment view

The 3DM superfamily is divided into subfamilies, with each subfamily consisting of a cluster of proteins that share a similar structure. By default, a superfamily alignment only shows the consensus of each aligned subfamily (identified by a representative PDB ID).

By clicking on a subfamily ID, the consensus can be expanded to view the protein sequences present in that subfamily.

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Consensus view
Subfamily view

Show/hide proteins

Show or hide first 15 proteins of all subfamilies.

Protein selection

Select what type of proteins should be shown:

• Structures excluded (default),
• Structures included,
• Structures only or
• 95% Clustered representatives.

Variable regions