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Metabolic Reconstruction

We use the term metabolic reconstruction to mean the set of populated subsystems that contain the genome, the Protein Encoding Genes that are connected to Functional Roles in these populated subsystems, and the specific variant associated with the genome in each of the populated subsystems.

In other words, the metabolic reconstruction comprises the subsystem-related data in the Sprout Database for a particular genome.

In the diagram below, the portion of the Sprout Database that makes up a metabolic reconstruction has been shaded yellow. Note that while both genomes and features are included, the relationship between them is not: in a metabolic reconstruction, the only features of interest are the ones in subsystems, and these are all connected to the SSCell entity.

Metabolic reconstruction data in the sprout database

In the NMPDR, you can compare the metabolic reconstructions of two genomes using the Compare Subsystems page. This brings up a side-by-side comparison of subsystems in both organisms, showing where they differ and where they match.

Topic revision: r3 - 16 Jan 2009 - 15:09:39 - Bruce Parrello

Notice to NMPDR Users - The NMPDR BRC contract has ended and bacterial data from NMPDR has been transferred to PATRIC (http://www.patricbrc.org), a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. NMPDR is funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract HHSN266200400042C. Banner images are copyright © Dennis Kunkel.