Data repository for Analysis of the cyanobacterial amino acid metabolism with a precise genome-scale metabolic reconstruction of Anabaena sp. UTEX 2576

Published: 04-03-2021| Version 1 | DOI: 10.17632/pfpgv2pc4p.1
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Description

This repository contains the data sets and source files associated with the research paper entitled "Analysis of the cyanobacterial amino acid metabolism with a precise genome-scale metabolic reconstruction of Anabaena sp. UTEX 2576" by Daniel A. Noreña-Caro, Cristal Zuñiga, Amber J. Pete, Sven A. Saemundsson, Morgan R. Donaldson, Alexandria J. Adams, Kerry M. Dooley, Karsten Zengler and Michael G. Benton The content of each data set is described in the main manuscript.

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Repository contains a genome scale metabolic model constructed from ModelSEED automatic reconstruction software and curated to adjust to the BiGG standard. Model files contain information from KEGG, Uniprot, PATRIC, Metacyc, and BRENDA. Model was analyzed with COBRA toolbox for MATLAB. Biomass equations and model constraints were experimentally determined with UV-visible spectroscopy, gas chromatography, flow cytometry, and electronic microscopy techniques. The repository also contains thermodynamic analysis of carbon dioxide equilibrium with bicarbonate ions. Biomass composition was statistically analyzed to determine the set of data used for construction biomass equations. The biomass equations were constructed as described in the main manuscript, following a methodology adapted from a model for Synechocystis sp. PCC 6803 (https://www.pnas.org/content/109/7/2678). FBA and FVA scripts are included in the repository. Data sets 2 and 3 contain blank versions of photoautotrophic and photodiazotrophic models, which do not constrain the solution to the experimental observations.