Structure based multiple sequence alignment (SB-MSA)

3DM uses a structure based MSA to connect the proteins of a superfamily. Via the alignment it is possible to transfer residue and alignment data to other proteins or structures.

In the alignment viewer you can view and analyse this alignment.

Consensus view

By default, a superfamily alignment only shows the consensus of each alignment subfamily. A subfamily is usually based on a protein structure and connected to other alignment subfamilies via the structural alignment.

The consensus can be expanded to view the protein sequences present in a subfamily.


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Consensus view(tick)(tick)(tick)
Subfamily view


Show/hide proteins

Only available in consensus view.

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

Only available in subfamily view.