BRENDA in 2015: exciting developments in its 25th year of existence

Abstract

The BRENDA enzyme information system (http://www.brenda-enzymes.org/) has developed into an elaborate system of enzyme and enzyme-ligand information obtained from different sources, combined with flexible query systems and evaluation tools. The information is obtained by manual extraction from primary literature, text and data mining, data integration, and prediction algorithms. Approximately 300 million data include enzyme function and molecular data from more than 30,000 organisms. The manually derived core contains 3 million data from 77,000 enzymes annotated from 135,000 literature references. Each entry is connected to the literature reference and the source organism. They are complemented by information on occurrence, enzyme/disease relationships from text mining, sequences and 3D structures from other databases, and predicted enzyme location and genome annotation. Functional and structural data of more than 190,000 enzyme ligands are stored in BRENDA. New features improving the functionality and analysis tools were implemented. The human anatomy atlas CAVEman is linked to the BRENDA Tissue Ontology terms providing a connection between anatomical and functional enzyme data. Word Maps for enzymes obtained from PubMed abstracts highlight application and scientific relevance of enzymes. The EnzymeDetector genome annotation tool and the reaction database BKM-react including reactions from BRENDA, KEGG and MetaCyc were improved. The website was redesigned providing new query options.

Figure 1.

The workflow for the construction of enzyme word maps illustrated for γ-glutamyltransferase (EC 2.3.2.2).

Figure 2.

The distribution of thymidylate synthases (EC 2.1.1.45 and EC 2.1.1.148) in bacteria and archaea obtained from the EnzymeDetector, mapped on the NCBI taxonomic tree. Only thymidylate synthase annotations with a relevance score above 8 were included. The relevance score reflects the sum of the weights of the different annotation sources. In this scheme, manual annotations (e.g. BRENDA) get high rates, whereas predictions get low ones. For a detailed description see (7).

Figure 3.

Enzymes in the pathway for the synthesis of pyrimidine deoxyribonucleotides detected by the EnzymeDetector, showing alternate routes. Red and light blue squares and rectangles represent alternate enzymes. Enzymes common to all pathway variants are shown in dark blue. The columns from left to right represent subsequent reaction steps.

Figure 4.

CAVEman human anatomy linked to enzyme data.