Reconstruction of Amino Acid Biosynthesis Pathways from the Complete GenomeâSequence Export

@article{citeulike:133451, abstract = {10.1101/gr.8.3.203 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 and and probably in and as well, although it was necessary to assume wider substrate specificity for aspartate aminotransferases.}, address = {Institute for Chemical Research, Kyoto University, Uji, Kyoto 611, Japan.}, author = {Bono, Hidemasa and Ogata, Hiroyuki and Goto, Susumu and Kanehisa, Minoru}, booktitle = {Genome Research}, citeulike-article-id = {133451}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.8.3.203}, citeulike-linkout-1 = {http://genome.cshlp.org/content/8/3/203.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/8/3/203.full.pdf}, citeulike-linkout-3 = {http://www.genome.org/cgi/content/abstract/8/3/203}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/9521924}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=9521924}, day = {1}, doi = {10.1101/gr.8.3.203}, issn = {1088-9051}, journal = {Genome Res}, keywords = {enzyme\_prediction}, month = {March}, number = {3}, pages = {203--210}, posted-at = {2008-10-07 15:04:30}, priority = {5}, title = {Reconstruction of Amino Acid Biosynthesis Pathways from the Complete Genome\^{a}€‰Sequence}, url = {http://dx.doi.org/10.1101/gr.8.3.203}, volume = {8}, year = {1998} }

TY - JOUR ID - citeulike:133451 L3 - citeulike-article-id:133451 N2 - 10.1101/gr.8.3.203 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 and and probably in and as well, although it was necessary to assume wider substrate specificity for aspartate aminotransferases. IS - 3 JF - Genome Res SN - 1088-9051 AD - Institute for Chemical Research, Kyoto University, Uji, Kyoto 611, Japan. EP - 210 TI - Reconstruction of Amino Acid Biosynthesis Pathways from the Complete Genome Sequence VL - 8 T2 - Genome Research SP - 203 KW - enzyme_prediction AU - Bono, Hidemasa AU - Ogata, Hiroyuki AU - Goto, Susumu AU - Kanehisa, Minoru PY - 1998/03/01/ UR - http://dx.doi.org/10.1101/gr.8.3.203 ER -