The database provides an original classification of whole proteins rather than their individual domains. It includes three levels of hierarchy:

  1. Functional class: receptors, ligands/regulators, structural/adhesion, proteins involved in biogenesis, membrane remodeling and vesicular trafficking, molecular transport, gene regulation, 6 classes of enzymes, and proteins with undefined function

  2. Superfamily: related proteins with similar domain architecture

  3. Family: proteins with significant sequence homology

Assignment to functional class is based on annotations from UniProt, Pfam, InterPro and publications.

Protein superfamilies generally correspond to clans or families in Pfam, MEROPS, and CAZy.

Allocation to protein families follows InterPro and UniProt classifications. Some proteins were assigned to families using Panther, InParanoid, and KEGG paralogues and orthologues. Different subunits of stable multiprotein complexes were included as families of the same superfamily.

Membranome also provides complexes formed by TM and/or water-soluble domains of bitopic proteins from the PDB. The complexes are classified into functional classes and families, similar to that for individual proteins.