Metabolism Tools

KEGG is an integrated database resource, broadly categorized into systems information, genomic information, and chemical information.
This page gives the list of KEGG metabolic pathways from which a least one enzymatic activity is predicted in the genome. Both annotated EC numbers and KEGG Orthology family predictions (KOfamScan software) are used to map the genes to their corresponding enzymatic activities.
Pathways are highlighted in red if they are associated with genes from the corresponding selected genomic region. Their number is indicated in brackets.
MicroCyc is a collection of microbial Pathway/Genome Databases (PGDBs) which are created in the context of the MicroScope projects. They are supported by the Pathway tools software developed by Peter Karp and his team at SRI international. These PGDBs were generated using the PathoLogic module which computes an initial set of pathways by comparing a genome annotations to the metabolic reference database MetaCyc.

For each studied genome, the annotation data is extracted from our Prokaryotic Genome DataBase (PkGDB) which benefit both the (re)annotation process performed in our group (AGC), the enzymatic function prediction computed with the PRIAM software, and the expert work for functional annotation made by a various community of biologists using the MaGe system. These automatically generated PGDBs (Tier3) are updated every day.
Starting with the set of KEGG or MicroCyc metabolic pathways predicted for each genome integrated in the PkGDB database, this method compares the metabolic content of the selected bacterial genomes. This comparison is based on the computation of a 'pathway completion' value i.e, the number of reactions for pathway x in a given organism/total number of reactions in the same pathway x defined in the MetaCyc or KEGG databases. To get an overview of the way compared genomes are clustered according to their metabolic capabilities, the MeV tool has been integrated to this functionality: it takes the result comparisons as input and performs a hierarchical clustering using the pathway completion values.

Starting from a list of MicroCyc pathways predicted by the Pathway Tools software, users are able to curate the prediction for a given organism by assigning different status.

Distinct pathway status are:

  • predicted: predicted by the BioCyc pathologic algorithm (default one)
  • validated: curated as a functional pathway (all the reactions of the pathway are supposed to exist in the organism)
  • variant needed: the predicted pathway is not completely correct for the organism (i.e. some reactions may not be present in the organism but no better pathway definition exists in MetaCyc). Thus, a new pathway variant definition is needed.
  • unknown: not enough evidence to declare the pathway as functional (i.e. validated status)
  • non functional: the pathway has been lost in the organism and is no more functional (i.e. due to gene loss or pseudogenisation events)
  • deleted: curated as a false positive prediction
AntiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. For each genome, data are extracted from our Prokaryotic Genome DataBase (PkGDB). The cluster visualization page can be accessed from this page, to know more about a specific antiSMASH predicted cluster.
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