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The hidden universal distribution of amino acid biosynthetic networks: a genomic perspective on their origins and evolution

Georgina Hernández-Montes1, J Javier Díaz-Mejía12, Ernesto Pérez-Rueda1 and Lorenzo Segovia1*

Author Affiliations

1 Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad, Col. Chamilpa, Cuernavaca, Morelos, México, CP 62210

2 Department of Biology, Wilfrid Laurier University, University Av. Waterloo, ON N2L 3C5, Canada; and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto. College St., Toronto, ON M5S 3E1, Canada

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Genome Biology 2008, 9:R95  doi:10.1186/gb-2008-9-6-r95

Published: 9 June 2008

Additional files

Additional data file 1:

As a complement to Figure 1, this file contains a detailed graph of the amino acid biosynthetic network analyzed in this work, including substrates and products. Additional data file 4 contains the network in xgmml format.

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Open Data

Additional data file 2:

Details on the 537 enzyme functional domains catalyzing 188 reactions in the biosynthesis of amino acids in diverse species according to EcoCyc, MetaCyc and MjCyc. The following details are provided: participating pathway(s); code for participating reactions in EcoCyc, MjCyc and MetaCyc; EC number(s); isoenzymes, multimeric components and analog enzymes; original species bearing the enzyme; genome carrying the enzyme; GI of genomic sequence; amino acid sequence - split in multifunctional enzymes; structural domains; average normalized distribution of orthologs across genomes; phylogenetic profile. Additionally, tables on the genomes included in this study, the connectivity of compounds and the node pairs forming the network in Figure 1 are provided.

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Open Data

Additional data file 3:

Detailed view from Figure 1 for pathways in the following order: (a) Arg, (b) Gly-Thr, (c) Trp, (d) Pro, (e) Ile-Val-Leu, (f) His, (g) Glu-Gln, (h) Ala-Cys-Ser-Met, (i) Lys, (j) Cor, (k) Asp/Asn, (l) Phe/Tyr. Nomenclature is as in Figure 1.

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Additional data file 4:

Bipartite graph of the final metabolic network analyzed in this work (after hub and end compounds removal).

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Open Data