ARAMEMNON database of plant membrane proteins

ARAMEMNON database of plant membrane proteins provides an integrated resource that identifies and annotates membrane proteins by combining transmembrane (TM) span and signal peptide predictions to support functional and comparative analyses in Arabidopsis thaliana and selected non-Arabidopsis proteins.

Key Features:

• Integration of Prediction Programs: Averages predictions from seven transmembrane (TM) span computation programs to classify approximately 6,500 proteins as TM candidate proteins.
• Identification of Transport-Related Proteins: Flags around 1,800 proteins with at least four TM spans as likely transport-related candidates.
• Comparative Prediction Outputs: Presents prediction results from seven TM span programs alongside outputs from eight signal peptide recognition programs for direct comparison.
• Dynamic Protein Family Structure Generation: Displays proteins related to a query and dynamically generates protein family structures for functional and evolutionary inspection.
• Inclusion of Non-Arabidopsis Proteins: Incorporates approximately 700 putative membrane proteins from the cyanobacterium Synechocystis sp. for comparative analyses.

Scientific Applications:

• Functional Annotation: Uses combined TM span and signal peptide predictions to support annotation of membrane protein topology and subcellular localization.
• Transport Function Studies: Identifies multi-pass membrane proteins (≥4 TM spans) that are candidate transporters for studying nutrient uptake, signaling, and stress responses.
• Comparative Genomics: Enables cross-species comparison between Arabidopsis thaliana and Synechocystis sp. to investigate evolutionary conservation of membrane proteins.
• Protein Family Analysis: Produces dynamic protein family structures to facilitate analysis of domain architecture, homology, and evolutionary relationships.

Methodology:

Integrates and averages predictions from seven TM span computation programs and incorporates outputs from eight signal peptide recognition programs to refine subcellular localization; additionally generates dynamic protein family structures from related protein sets.