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

Chang A, Schomburg I, Placzek S, Jeske L, Ulbrich M, Xiao M, Sensen CW, Schomburg D - Nucleic Acids Res. (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Langer Kamp 19 B, D-38106 Braunschweig, Germany.

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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).
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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).

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 2.1.1.45 and EC 2.1.1.148) 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 2.1.1.45. The classes Actinobacteria, Chlamydia and Clostridia predominately express EC 2.1.1.148, 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 2.1.1.148.


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

Chang A, Schomburg I, Placzek S, Jeske L, Ulbrich M, Xiao M, Sensen CW, Schomburg D - Nucleic Acids Res. (2014)

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).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383907&req=5

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).
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 2.1.1.45 and EC 2.1.1.148) 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 2.1.1.45. The classes Actinobacteria, Chlamydia and Clostridia predominately express EC 2.1.1.148, 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 2.1.1.148.

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Langer Kamp 19 B, D-38106 Braunschweig, Germany.

Show MeSH
Related in: MedlinePlus