We present a dataset of large redundant and non-redundant rumen microbial protein predictions, and provide rich annotation using public protein, pathway and enzyme databases. This resource will enable researchers to predict the function of each protein, and better assess the functional consequences of ...
KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 40, D109–D114 (2012). Article CAS PubMed Google Scholar Caspi, R. et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic ...
Yet, there is still a significant gap in our knowledge of metabolic networks, particularly for organism-specific pathways, as many pathways are missing from current pathway databases. Computational approaches play an important role in bridging this gap. Prediction of metabolic pathways consisting of ...
and specificities to identify an enzyme exhibiting activity towards a required pathway intermediate. For example, in the synthesis of non-natural alcohols, the Liao group screened 7 different ketoacid decarboxylases from four different organisms before identifying KIVD as a broad substrate range ketoacid...
databases. Bioinformatic tools to select genes have been getting more sophisticated. Originally, only sequence similarity to a target enzyme guided the search using algorithms such as the Basic Local Alignment Search Tool (BLAST)[78,83–95]. Metabolic databases have compiled reaction and pathway ...
The first approach combines bioinformatics and molecular modelling to mine sequence databases, resulting in a diverse panel of enzymes capable of catalysing the targeted reaction. The median catalytic efficiency of the computationally selected enzymes is 75-fold greater than a panel of naively selected ...
and maintain the growth and survival of cells. According to widespread opinion, most cascades in metabolic pathways are spatially bound by non-covalent protein–protein interactions (PA1987; You2012). Cascade enzymes are close to each other in space in the metabolic pathway of organisms and form ...
The tool generated both nucleotide sequences and protein sequences in file formats for further analysis. Functional annotation and pathway analysis The functional diversity within these metagenomes was explored by analyzing the predicted coding sequences using the InterPro database via the InterProScan ...
instance, the sequence database UniProt contains over 230 million enzyme sequences, while enzyme databases BRENDA and SABIO-RK contain tens of thousands of experimentally measuredkcatvalues6,7,8. The integration of Uniprot identifiers in these enzyme databases has facilitated the connection between ...
Tandem MS spectra of newly reported structures are available in the Supplementary Note and were also deposited to the GNPS spectral library at the URLs shown in the Supplementary Note. The following bioinformatic databases were employed in this study: BRENDA (https://www.brenda-enzymes.org/), ...