Again a subsystem hierarchy can be un-collapsed and for each subsystem that has been asserted, a scenario is given with input and output compounds, their stoicheometry and a relevant coloured KEGG map (if one exists).
From Metabolite to Metabolite (FMM) is a web server freely available at http://FMM.mbc.nctu.edu.tw/ that is able to search all possible pathways between known input and output compounds among various species based on the KEGG database and other integrated biological databases [ 20].
The homology score of a given mapping can be defined in terms of the similarities of input compounds, output compounds and enzymes of R x and.
The homology score of is then defined as a convex combination of the scores attained from the scores calculated independently for the enzymes, input compounds and output compounds.
BioDICE has generated an interactive map of the input compounds and a list of the compounds in each detected cluster.
Similar constructions can be carried out for the unions of input compounds, and the unions of output compounds.
The plugin also accepts two optional inputs, which are used for enriching the graphical representation of the chemical compounds: an ordered list of input compounds and a list of their corresponding representations in SMILES notation.
To that end, the notion of pathway – defined unambiguously as the conversion between specified sets of input compounds (reactants) and output compounds (products) – can bring a useful decomposition of metabolism into basic biochemical functional units, in the spirit pioneered by SEED (Overbeek et al., 2005), KEGG Modules (Kanehisa et al., 2007), or MetaCyc (Caspi et al., 2006).
The job ID of this test example was 'eg_NAD' and the input was compound list (C00003: NAD+).
However, these applications could come without public input and could allow a compounded environmental risk to go unexamined, environmental groups warn.
