Guidance for metabolic maps

List of shapes used in the metabolic pathway maps


Shape Description

Any commodity metabolite in the reactions (main substrates and products and does not include the cofactors). It does not include protein, DNA and RNA metabolites
Simple molecules as aliased metabolites or compounds. They are also known as currency metabolites. These are co-substrates and co-products including cofactors.
Proteins including enzymes as commodity metabolites (main substrates and products) in reactions
Protein molecules as aliased metabolites or compounds. These are proteins which undergo modification in the reaction and act as co-substrates or co-products.
Cations (mainly H+, Ca2+) as aliased metabolites in reactions
tRNAs and aminoacyl-tRNAs
mRNAs as metabolites in reactions
Monofunctional enzymes (single EC number annotation)
Enzymes which should be present in the organism to provide complete metabolic pathway, but, gene is missing in the present gene models.
Multifunctional enzymes. The figure shows a bifunctional enzyme with two EC number annotations. The outer rectangle  represents a single protein (gene) and the inner rectangles represent each function (single EC number).
Multimodule containing multifunctional enzyme. The figure shows a multifunctional enzyme (from single gene) with two modules. Each module might have more than 1 enzyme function (more than 1 EC numbers). There can be more than one module of same function as in the case of FASI. The only example of this category in these metabolic pathways is FASI (
Multiprotein complex/Multi-subunit protein - Each protein complex has more than one polypeptides (encoded by more than 1 genes) carrying out same or different functions. This is used in electron transport chain pathway for different mitochondrial complexes.
Non-enzymatic proteins (not even partial EC numbers). E.g. Acyl-CoA binding protein, transcription factors etc.
Proteins annotated to known transporter functions.


List of reaction types used in the metabolic pathway maps