TSdb: A database of transporter substrates linking metabolic pathways and transporter systems on a genome scale via their shared substrates
- 651 Downloads
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.
Keywordstransporter substrate biological database compound classification compound metabolic network
- 1.Nelson D L, Cox M M. Lehninger’s principles of biochemistry. 3rd ed. New York: Worth Publishers, 2000Google Scholar
- 20.Lu Z, Cohen K B, Hunter L. GeneRIF quality assurance as summary revision. Pac Symp Biocomput, 2007, 269-280Google Scholar
- 25.Willis R C, Hogue C W. Searching, viewing, and visualizing data in the Biomolecular Interaction Network Database (BIND). Curr Protoc Bioinformatics online publication 1 January 2006; doi: 10.1002/0471250953.bi0809s12Google Scholar
This article is published under license to BioMed Central Ltd. Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution and reproduction in any medium, provided the original author(s) and source are credited.