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Comparative Study
. 2003 Nov;13(11):2455-66.
doi: 10.1101/gr.1212003. Epub 2003 Oct 14.

In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism

Masanori Arita  1
Affiliations
Comparative Study

In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism

Masanori Arita. Genome Res. 2003 Nov.

Abstract

We present a software system that computationally reproduces biochemical radioisotope-tracer experiments. It consists of three main components: A mapping database of substrate-product atomic correspondents derived from known reaction formulas, a tracing engine that can compute all pathways between two given compounds by using the mapping database, and a graphical user interface. As the system can facilitate the display of all possible pathways between any two compounds and the tracing of every single carbon, nitrogen, or sulfur atom in the metabolism, it complements and bridges other metabolic databases and simulations on fixed models.

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Figures

Figure 1
Figure 1
The reaction by transaldolase (EC 2.2.1.2).
Figure 2
Figure 2
The reaction by serine-pyruvate aminotransferase (EC 2.6.1.51).
Figure 3
Figure 3
Three reactions in the pentose-phosphate pathway. Two are catalyzed by transketolase (EC 2.2.1.1) and the other by transaldolase (EC 2.2.1.2). Dotted lines connect equivalent metabolites. (Left panel) The conventional description. (Right panel) Proposed graph representation in which each reaction corresponds to three mappings.
Figure 4
Figure 4
Two reactions by transketolase (EC 2.2.1.1).
Figure 4
Figure 4
Two reactions by transketolase (EC 2.2.1.1).
Figure 5
Figure 5
A valid pathway from Xyl5P to Ery4P. Positions highlighted in red show the conserved moiety (carbon atoms) in this pathway.
Figure 6
Figure 6
Two displays of the same pathway from Xyl5P to Ery4P.
Figure 7
Figure 7
The number of reactions, mappings, and EC sub-subclasses in the reference metabolism against the total number of EC sub-subclasses in the LIGAND database. The blue, red, and yellow bars (%reactions, %mappings, and %EC classes, respectively) signify the percent contribution of each EC class for all reactions, mappings, and EC sub-subclasses in the reference metabolism (the six classes total 100%); the skyblue bar (%reactions) signifies the percent contribution of the EC sub-subclasses in the LIGAND database.
Figure 8
Figure 8
The number of reactions, mappings, and EC sub-subclasses in the E. coli metabolism against the total number of EC sub-subclasses in the EcoCyc database. Colors conform to those in Fig. 7.
Figure 9
Figure 9
Relevant subgraph between l-Asp and l-Ala. Blue arrows signify reactions annotated for E. coli in the KEGG database, and green dashed arrows are reactions not annotated in E. coli. Numbers beside the arrows are ECs for enzymes.
Figure 10
Figure 10
Two pathways from l-Asp to l-Ala in the E. coli metabolism. Positions highlighted in purple show the conserved nitrogen atoms in these pathways.
Figure 11
Figure 11
Entry 1.1.1.1 in the LIGAND database.
Figure 12
Figure 12
Mapping information between allantoin and allantoate.
Figure 13
Figure 13
The pathway from d-glucose to secologanin. Positions highlighted in red show the conserved carbon atoms in this pathway.
See this image and copyright information in PMC

References

    1. Abe, K., Ohnishi, F., Yagi, K., Nakajima, T., Higuchi, T., Sano, M., Machida, M., Sarker, R.I., and Maloney, P.C. 2002. Plasmid-encoded asp operon confers a proton motive metabolic cycle catalyzed by an aspartate-alanine exchange reaction. J. Bacteriol. 184: 2906-2913. - PMC - PubMed
    1. Arita, M. 2000a. Metabolic reconstruction using shortest paths. Simulation Pract. Theory 8: 109-125.
    1. Arita, M. 2000b. Graph modeling of metabolism. J. Jpn. Soc. Artif. Intell. (JSAI) 15: 703-710.
    1. Arita, M., Asai, K., and Nishioka, T. 2000. Reconstructing metabolic pathways with new enzyme classification. In Proceedings German Conf. Bioinformatics (GCB'00), pp. 99-106. Heidelberg, Germany.
    1. Budavari, S., O'Neil, M.J., Smith, A., Heckelman, P.E., and Kinneary, J.F. eds. 1996. Merck index: An encyclopedia of chemicals, drugs, and biologicals, 12th ed. Merck, NJ.

WEB SITE REFERENCES

    1. http://us.expasy.org/enzyme; ENZYME database.
    1. http://www.brenda.uni-koeln.de; BRENDA database.
    1. http://www.chem.qmul.ac.uk/iubmb/enzyme; IUBMB enzyme nomenclature.
    1. http://www.ecocyc.org; EcoCyc database.
    1. http://www.mdli.com; MDL Information Systems.

MeSH terms