BRENDA in 2015: exciting developments in its 25th year of existence.
Bottom Line: New features improving the functionality and analysis tools were implemented.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.
Affiliation: Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Langer Kamp 19 B, D-38106 Braunschweig, Germany.Show MeSH
Related in: MedlinePlus
Mentions: The newly designed EnzymeDetector website offers various ways to explore enzyme diversity within the database. The enzyme repertoire of whole phylogenetic clades can be analyzed (27,28). Figure 2 shows the distribution of the two thymidylate synthases (EC 220.127.116.11 and EC 18.104.22.168) in bacteria and archaea as obtained from EnzymeDetector, mapped on the taxonomic tree of the NCBI. These enzymes catalyze an essential step in the synthesis of pyrimidine deoxyribonucleotides. Several alternate pathways are observed which differ in the usage of the two key enzymes. β- and γ-proteobacteria, enterobacteria and bacilli are restricted to the use of EC 22.214.171.124. The classes Actinobacteria, Chlamydia and Clostridia predominately express EC 126.96.36.199, with tightly bound flavin adenine dinucleotide (FAD). Archaea, which are known for their metabolic versatility, are clearly split into two groups, using either the classical branch or displaying the alternate path with EC 188.8.131.52.
Affiliation: Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Langer Kamp 19 B, D-38106 Braunschweig, Germany.