Castillo2016 - Whole-genome metabolic model of M.grisea using CoReCo

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

本模型基于CoReCo方法（CoReCo），利用蛋白质序列与系统发育数据重构得到。CoReCo方法的相关文献参见：Pitkanen, E., Jouhten, P., Hou, J., Syed, M. F., Blomberg, P., Kludas, J., Oja, M., Holm, L., Penttilä, M., Rousu, J. 及 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 以及 Castillo, S., Barth, D., Arvas, M., Pakula, TM., Pitkanen, E., Blomberg, P., Penttilä M., Oja M. Whole genome metabolic model of Trichoderma reesei built by comparative reconstruction.
CoReCo可为每条反应标注如下属性：
reco:balanced：若反应符合化学计量平衡，则取值为True；
reco:posterior：CoReCo第二阶段的后验概率；
reco:cost：CoReCo第二阶段的对数评分；
reco:level：当评分低于重构阈值时标记为High（高），高于阈值时标记为Low（低）。仅带有Low等级的反应会在重构过程中用于填补High等级反应的代谢缺口；
reco:naivep：CoReCo第一阶段的概率；
reco:btscore：仅以BLAST作为输入时，CoReCo第二阶段的后验概率；
reco:gtscore：仅以GTG作为输入时，CoReCo第二阶段的后验概率；
reco:bscore：CoReCo的BLAST评分；
reco:bseq1：目标物种中BLAST评分最高的蛋白质序列；
reco:bseq2：UniProt数据库中BLAST评分最高的蛋白质序列；
reco:gscore：CoReCo的GTG评分；
reco:gseq1：目标物种中的蛋白质序列；
reco:gseq2：GTG数据库中GTG评分最高的蛋白质序列