Metabolic data of endosymbiontic, parasitic and free bacteria
Endosymbiont bacteria, which live inside the cells of their host, in intimate association with the latter, have a very simplified metabolism, corresponding to a drastic reduction of the genome compared to the genome of the phylogenetically related free bacteria. Several main metabolic functions are therefore provided by the host. However, some of those functions, such as the ones involved in the symbiotic association, are maintained in the metabolism of the bacterium. In addition, the metabolic network of an endosymbiont should exhibit topological properties which reflect the predominance of some metabolic compounds or biochemical reactions. To understand which properties depend on the symbiotic characteristic of the bacterium, it is important to compare these properties among bacteria having different life style. SymbioCyc proposes a direct access to the metabolic network of several endosymbionts but also of free and parasitic bacteria through a BioCyc-like interface. When the metabolic network of an organism does not belong to the list of the expert-curated databases of BioCyc, genomic annotations have been computed with the Microbial Genome Annotation System of the Genoscope and used to infer the list of the possible enzymatic reactions with the Pathway Tools Software. Each database is available in SBML format and to facilitate the analysis of the networks, reaction and compound graphs are also made available in Cytoscape format. SymbioCyc further provides some basic descriptive statistics on each metabolic network. Moreover, an interface allows for an easy comparison of the lists of compounds, reactions and pathways between several organisms or between several sets of organisms, based not on individual differences but on differences between groups of organisms sharing a same property such as life style.

Features:

  1. Metabolic networks of each organism are available in different formats:
    • SBML files containing informations about links between genes, proteins, and reactions. Click here to see the specifications of the format. These files are readable by every software allowing SBML reading. Visite the official site of SBML to obtain an exhaustive list of these softwares.

    • Different graphical representations:
      1. The graph of reactions (directed or undirected): the nodes are the reactions and it exists one edge between two reactions if at least one product of one reaction is the substrate of the other. This representation takes into account the reversibility of the reactions. If the graph is directed, then two reactions are linked by two directed edges if both are reversible. If the graph is undirected, in this case the two reactions will be linked by only one edge.
      2. The graph of compounds (directed or undirected): the nodes are the compounds and it exists one edge between two compounds if at least one compound can be produced from the other by one reaction. This representation takes also into account the reversibility of the reactions. If the graph is directed, and if two compounds are linked by one reversible reaction then they are linked by two directed edges. If the graph is undirected, in this case, the two compounds are linked by only one edge.
      3. The bipartite graph (directed): two types of nodes: the reactions and the compounds. One reaction node can be only linked with compound nodes and one compound node can be only linked with reaction nodes.

      Each graphical representation is available in the "sif" format, the original network format of Cytoscape, which is simply a list of edges between nodes.

  2. Two possible filters are available on each dataset

    • Keep only the reactions which occur in a metabolic pathway and the compounds annotated as primary
    • Remove the reactions that involve generic compounds (ex : an aldehyde)

  3. Global properties of each dataset :

    • List of the 30 most frequent compounds
    • Distribution of the number of reactions where each compound occur
    • Distribution of the number of pathways where each reaction occurs
    • Distribution of the number of substrates and products occuring per reaction
    • Distribution of the number of enzyme per reaction
    • Distribution of the number of reactions catalysed by each enzyme
    • Proportion of the first class of the EC numbers

  4. The link on the corresponding BioCyc-like PGDB, build by other teams or by the Baobab team when the PGDB is not curated by any other team. Of course, each PGDB is available on demand.

  5. An interface allows for an easy comparison of the lists of compounds, reactions and pathways between several organisms or between several sets of organisms, based not on individual differences but on differences between groups of organisms sharing a same property such as life style.



Please read the documentation to have an overview of the capacities of SymbioCyc and to know how to use it !