Castillo2016 - Whole-genome metabolic model of U.maydis using CoReCo

ABSTRACT: This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkanen, E., Jouhten, P., Hou, J., Syed, M. F., Blomberg, P., Kludas, J., Oja, M., Holm, L., Penttila, M., Rousu, J. and Arvas, M. (2014). Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species. PLoS Computational Biology, 10(2), e1003465. doi:10.1371/journal.pcbi.1003465 and Castillo, S., Barth, D., Arvas, M., Pakula, TM., Pitkanen, E., Blomberg, P., Penttila M., Oja M. Whole genome metabolic model of Trichoderma reesei built by comparative reconstruction. CoReCo annotates each reaction with the following attributes: reco:balanced: True, if reaction is in stoichiometric balance. reco:posterior: CoReCo phase II probability reco:cost: CoReCo phase II log-score reco:level: High, if cost below reconstruction threshold, and Low, if cost above reconstruction threshold. A reaction with level=Low only appears in reconstruction to gapfill a reaction with level=High. reco:naivep: CoReCo phase I probability. reco:btscore: CoReCo phase II probability considering only BLAST as input. reco:gtscore: CoReCo phase II probability considering only GTG as input. reco:bscore: CoReCo BLAST score reco:bseq1: Protein sequence in target species with highest BLAST score reco:bseq2: Protein sequence in UniProt with highest BLAST score reco:gscore: CoReCo GTG score reco:gseq1: Protein sequence in target species reco:gseq2: Protein sequence in GTG database with highest GTG score

SUBMITTER: Vijayalakshmi Chelliah  

PROVIDER: MODEL1604280020 | BioModels | 2016-12-02

REPOSITORIES: BioModels