Castillo2016 - Whole-genome metabolic model of A.clavatus 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

本模型基于蛋白质序列与系统发育数据，通过CoReCo方法重构得到。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., Penttila, M., Rousu, J. 与 Arvas, M. (2014). 《现生与祖先物种无间隙代谢网络的比较基因组规模重构》, PLoS计算生物学, 10(2), e1003465. doi:10.1371/journal.pcbi.1003465
以及 Castillo, S., Barth, D., Arvas, M., Pakula, TM., Pitkanen, E., Blomberg, P., Penttila M., Oja M. 《基于比较重构方法构建的里氏木霉全基因组代谢模型》

CoReCo会为每个反应标注以下属性：
- `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第二阶段的对数得分
- `reco:level`：当得分低于重构阈值时为High（高），高于阈值时为Low（低）。等级为Low的反应仅在重构过程中出现，用于补隙等级为High的反应。
- `reco:naivep`：CoReCo第一阶段的概率
- `reco:btscore`：仅以BLAST（基础局部比对搜索工具）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得分
- `reco:bseq1`：目标物种中BLAST得分最高的蛋白质序列
- `reco:bseq2`：UniProt（通用蛋白质知识库）中BLAST得分最高的蛋白质序列
- `reco:gscore`：CoReCo的GTG得分
- `reco:gseq1`：目标物种中的蛋白质序列
- `reco:gseq2`：GTG数据库中GTG得分最高的蛋白质序列