Castillo2016 - Whole-genome metabolic model of L.elongisporus 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

ORGANISM(S): Lodderomyces elongisporus

SUBMITTER: Vijayalakshmi Chelliah 

PROVIDER: MODEL1604280039 | biostudies-other |

SECONDARY ACCESSION(S): 27895706

REPOSITORIES: biostudies-other