MicroScope - Tutorial   »   Metabolism   »   Metabolic Profile


How to access to the Metabolic Profile Tool ?

Metabolic Profile tool is accessible in the Metabolism section of the main navigation menu.

What is the usefulness of this tool ?

This method allows to:

  • compare the metabolic content of the selected bacterial genomes,
  • highlight common or specific metabolic pathways,
  • detect uncompleted network to fill with expert annotations.

This comparison is based on the computation of a ’pathway completion’ value, i.e the ratio between the number of reactions for pathway X in a given organism and the total number of reactions of pathway X defined in the MetaCyc or KEGG databases.

noriao.png (PNG)

How to use this tool ?

(PNG)
  • 1) Choose a metabolic database of reference (BioCyc/MicroCyc or Kegg).
  • 2) Select the organisms to compare (up to 15).
  • 3) Select the metabolic pathways of interest (some or all).
  • 4) Validation

The With pseudogenes option allows to include pseudogenes in the analysis

Use the Pathway Completion box to restrict the analysis to pathways with a completion higher than a threshold

How to read the result table ?

(PNG)
  • 1) Different Organisms chosen.
  • 2) Metabolic Pathways of interest.
  • 3) Completion of the pathway in this organism.
    • the « reaction number » column show the number of reactions forming the complete metabolic pathway.
    • cliking on the completion number open the BioCyc or KEGG metabolic map for this organism.

Reactions table

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Clicking on a metabolic pathway in the result table allows to access to the detailled reaction table of this pathway. This table summarizes for each selected organism the presence/absence of genes coding for enzymes necessary for each reaction of the pathway.

  • 1) Selected organisms.
  • 2) Reactions required to perform this metabolic pathway.
  • 3) Gene(s) coding for enzyme(s) implicated in this reaction for this organism. Pseudogenes are flagged with (pseudo) in this table.

The link below the table allows access to the BioCyc or KEGG comparison metabolic maps.