TSdb:A database of transporter substrates linking metabolic pathways and transporter systems on a genome scale via their shared substrates  

作　　者：ZHAO Min CHEN YanMing QU DaCheng QU Hong 

机构地区：[1]Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China [2]Key Laboratory of Evolutionary Systematics of Vertebrates, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China [3]School of Computer Science & Technology, Beijing Institute of Technology, Beijing 100081, China

出　　处：《Science China(Life Sciences)》2011年第1期60-64,共5页中国科学（生命科学英文版）

基　　金：supported by the National High Technology Research and Development Program of China (Grant Nos. 2006AA02Z334, 2006AA02Z314, 2006AA02A312 and 2007AA02Z165);the National Basic Research Program of China (Grant Nos. 2006CB910404 and 2007CB946904);support of the K. C. Wong Education Foundation, Hong Kong

摘　　要：TSdb (http://tsdb.cbi.pku.edu.cn) is the first manually curated central repository that stores formatted information on the substrates of transporters. In total, 37608 transporters with 15075 substrates from 884 organisms were curated from UniProt functional annotation. A unique feature of TSdb is that all the substrates are mapped to identifiers from the KEGG Ligand com- pound database. Thus, TSdb links current metabolic pathway schema with compound transporter systems via the shared compounds in the pathways. Furthermore, all the transporter substrates in TSdb are classified according to their biochemical properties, biological roles and subcellular localizations. In addition to the functional annotation of transporters, extensive compound annotation that includes inhibitor information from the KEGG Ligand and BRENDA databases has been integrated, making TSdb a useful source for the discovery of potential inhibitory mechanisms linking transporter substrates and metabolic enzymes. User-friendly web interfaces are designed for easy access, query and download of the data. Text and BLAST searches against all transporters in the database are provided. We will regularly update the substrate data with evidence from new publications.TSdb （http：//tsdb.cbi.pku.edu.cn） is the first manually curated central repository that stores formatted information on the substrates of transporters. In total, 37608 transporters with 15075 substrates from 884 organisms were curated from UniProt functional annotation. A unique feature of TSdb is that all the substrates are mapped to identifiers from the KEGG Ligand com- pound database. Thus, TSdb links current metabolic pathway schema with compound transporter systems via the shared compounds in the pathways. Furthermore, all the transporter substrates in TSdb are classified according to their biochemical properties, biological roles and subcellular localizations. In addition to the functional annotation of transporters, extensive compound annotation that includes inhibitor information from the KEGG Ligand and BRENDA databases has been integrated, making TSdb a useful source for the discovery of potential inhibitory mechanisms linking transporter substrates and metabolic enzymes. User-friendly web interfaces are designed for easy access, query and download of the data. Text and BLAST searches against all transporters in the database are provided. We will regularly update the substrate data with evidence from new publications.

关 键 词：transporter substrate biological database compound classification compound metabolic network 

分 类 号：TP311.13[自动化与计算机技术—计算机软件与理论] U656.117[自动化与计算机技术—计算机科学与技术]