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

Min Zhao; Y M Chen; D Qu; H Qu

doi:10.1007/s11427-010-4125-y

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

Journal article

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

Min Zhao, Y M Chen, D Qu and H Qu

Science China Life Sciences, Vol.54(1), pp.60-64

2011

DOI: https://doi.org/10.1007/s11427-010-4125-y

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Abstract

transporter substrate

biological database

compound classification

compound metabolic network

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 compound 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. © 2011 Science China Press and Springer-Verlag Berlin Heidelberg.

Details

Title: TSdb: A database of transporter substrates linking metabolic pathways and transporter systems on a genome scale via their shared substrates
Authors: Min Zhao (Author) - Peking University, China
Y M Chen (Author) - Peking University, China
D Qu (Author) - Peking University, China
H Qu (Author) - Peking University, China
Publication details: Science China Life Sciences, Vol.54(1), pp.60-64
Publisher: Zhongguo Kexue Zazhishe [Science China Press]
Date published: 2011
DOI: 10.1007/s11427-010-4125-y
ISSN: 1674-7305
Organisation Unit: School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; School of Science, Technology and Engineering; Centre for Bioinnovation
Language: English
Record Identifier: 99449206002621
Output Type: Journal article

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