DetoxiProt: an integrated database for detoxification proteins

Abstract

Background: Detoxification proteins are a class of proteins for degradation and/or elimination of endogenous and exogenous toxins or medicines, as well as reactive oxygen species (ROS) produced by these materials. Most of these proteins are generated as a response to the stimulation of toxins or medicines. They are essential for the clearance of harmful substances and for maintenance of physiological balance in organisms. Thus, it is important to collect and integrate information on detoxification proteins.

Results: To store, retrieve and analyze the information related to their features and functions, we developed the DetoxiProt, a comprehensive database for annotation of these proteins. This database provides detailed introductions about different classes of the detoxification proteins. Extensive annotations of these proteins, including sequences, structures, features, inducers, inhibitors, substrates, chromosomal location, functional domains as well as physiological-biochemical properties were generated. Furthermore, pre-computed BLAST results, multiple sequence alignments and evolutionary trees for detoxification proteins are also provided for evolutionary study of conserved function and pathways. The current version of DetoxiProt contains 5956 protein entries distributed in 628 organisms. An easy to use web interface was designed, so that annotations about each detoxification protein can be retrieved by browsing with a specific method or by searching with different criteria.

Conclusions: DetoxiProt provides an effective and efficient way of accessing the detoxification protein sequences and other high-quality information. This database would be a valuable source for toxicologists, pharmacologists and medicinal chemists. DetoxiProt database is freely available at http://lifecenter.sgst.cn/detoxiprot/.

Figure 1

Classification of the detoxification proteins in DetoxiProt. Detoxification proteins can be classified as Phase I, Phase II xenobiotic-metabolizing enzymes and antioxidant enzymes according to their functional mechanisms. Totally 20 protein families were identified. Some protein families can be classified as subfamilies, including the short-chain dehydrogenase/reductase and peroxidase.

Figure 2

Data source and integration of DetoxiProt. Protein sequences are mainly sourced from NCBI and SwissProt, Protein structures were retrieved from PDB database, Biochemical feature were predicted by ProtParam tool from the Expasy server, substrates, inducers and inhibitors for detoxification proteins were manually compiled from literature.

Figure 3

DetoxiProt Interface. (A) Description page for each protein class, (B) Protein query page of the database, (C) Bibliography browse page, (D) an example for search result of human GSTA1, protein entry DP00451, detailed information includes general information, protein features, protein sequences, protein structures and external database links.

Figure 4

Distribution of human detoxification proteins and related toxins documented in Detoxiprot. (A) Histogram of the number of toxins associated with individual detoxification protein, (B) Histogram of the number of detoxification proteins associated with individual toxin.