Castillo2016 - Whole-genome metabolic model of C.globosum 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，利用蛋白质序列与系统发育数据重构得到。CoReCo方法的相关研究文献如下： 1. Pitkanen E, Jouhten P, Hou J, Syed MF, Blomberg P, Kludas J, Oja M, Holm L, Penttila M, Rousu J, Arvas M. 2014年发表于《PLOS计算生物学》(PLoS Computational Biology)的《现有与祖先物种无缺口代谢网络的全基因组比较重构》(Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species)，卷10，期2，文章编号e1003465，DOI: 10.1371/journal.pcbi.1003465； 2. Castillo S, Barth D, Arvas M, Pakula TM, Pitkanen E, Blomberg P, Penttila M, Oja M. 《基于比较重构构建的里氏木霉全基因组代谢模型》(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第二阶段的概率值； - reco:cost：CoReCo第二阶段的对数评分； - reco:level：当评分低于重构阈值时为High（高），高于阈值时为Low（低）。等级为Low的反应仅用于填补等级为High的反应所存在的代谢网络缺口； - reco:naivep：CoReCo第一阶段的概率值； - reco:btscore：仅以基本局部比对搜索工具 (BLAST)作为输入时，CoReCo第二阶段的概率值； - reco:gtscore：仅以GTG作为输入时，CoReCo第二阶段的概率值； - 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：通用蛋白质知识库 (UniProt)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。