Introduction

The Membranome (Membrane Proteome) database was developed to assist in analysis and modeling of single-pass (bitopic) transmembrane (TM) proteins in membranes. The database currently holds structural and functional data of more than 6000 bitopic proteins encoded by genomes of organisms representing six kingdoms of life. It provides the following data:

  1. Evolutionary classification of bitopic proteins, along with their topology, intracellular localizations, structural domains and interactions with each other collected from different sources (see "Sources")
  2. Computationally generated 3D models of TM α-helices of bitopic proteins and their spatial arrangement in the lipid bilayer. Models are generated by FMAP (see "Methods")
  3. 3D structures of quaternary complexes formed by TM and water-soluble domains of bitopic proteins.

Database Access

Menu on the left side allows browsing of content for proteins or their complexes by classes, superfamilies, families, localizations in different membrane types, and species.

  • Each of the six proteomes can be accessed separately using "Select Species" button. Then the picture of the selected organism appears below the button. Please select "All" to return to browsing all organisms simultaneously.
  • The database can be searched using text (protein names, keywords), UniProt ID, and PDB IDs.
  • Sortable tables provide the following information:

  • "Family" (local ID), "Protein Name", "Protein ID" (from UniProtKB) and "Species";
  • "Topology", i.e. location of helix N-terminus at the inner or outer membrane side;
  • "TM Segment", i.e. location of TM segment and the entire alpha-helix (in parenthesis) in the amino acid sequence;
  • "Hydrophobic thickness" of the helix calculated by PPM program;
  • "Tilt angle", i.e. angle between axis and membrane normal;
  • ΔGfold - free energy of alpha-helix relative to coil in water calculated by FMAP;
  • ΔGtransf - energy of helix transfer from water to the membrane environment calculated by PPM.
  • See also Methods

    Download Membranome files provide the entire database in .sql and .txt formats and selected Tables and lists from the database. Protein lists are sorted by protein families (first and second fields). Fields in text Tables and lists are separated by "|".

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