Reconstruction of amino acid biosynthesis pathways from the complete genome sequence
Reconstruction of amino acid biosynthesis pathways from the complete genome sequence
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DOI：
10.1101/gr.8.3.203
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发表时间：
1998-03-01
期刊：
影响因子：
7
通讯作者：
Kanehisa, M
中科院分区：
文献类型：
--
作者：
Bono, H;Ogata, H;Kanehisa, M
生物的全基因组序列包含的信息在目前的基因功能预测方法中尚未被充分利用，这些预测方法是基于单个基因的逐块相似性搜索。我们在这里提出了一种方法，利用分子途径的更高水平的信息，从一组基因重建一个完整的功能单元。具体而言，首先进行基因组间的比较，以确定酶基因并分配EC编号，然后利用参考生化知识重建选定的代谢途径部分。重建途径的完整性是初始基因功能分配正确性的一个指标。这一功能之所以成为可能，是因为我们在KEGG项目下努力将代谢途径的现有知识电脑化。我们发现所有20种氨基酸的生物合成途径在大肠杆菌、流感嗜血杆菌和枯草芽孢杆菌中完全重建，可能在聚胞菌和酿酒酵母中也完全重建，尽管有必要对天冬氨酸转氨酶进行更广泛的底物特异性假设。
The complete genome sequence of an organism contains information that has not been fully utilized in the current prediction methods of gene functions, which are based on piece-by-piece similarity searches of individual genes. We present here a method that utilizes a higher level information of molecular pathways to reconstruct a complete functional unit from a set of genes. Specifically, a genome-by-genome comparison is first made for identifying enzyme genes and assigning EC numbers, which is followed by the reconstruction of selected portions of the metabolic pathways by use of the reference biochemical knowledge. The completeness of the reconstructed pathway is an indicator of the correctness of the initial gene function assignment. This feature has become possible because of our efforts to computerize the current knowledge of metabolic pathways under the KEGG project. We found that the biosynthesis pathways of all 20 amino acids were completely reconstructed in Escherichia coli, Haemophilus influenzae, and Bacillus subtilis, and probably in Synechocystis and Saccharomyces cerevisiae as well, although it was necessary to assume wider substrate specificity for aspartate aminotransferases.