UniProt: a hub for protein information

UniProt Consortium - Nucleic acids research, 2015 - academic.oup.com
UniProt is an important collection of protein sequences and their annotations, which has
doubled in size to 80 million sequences during the past year. This growth in sequences has …

Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli

DC Sévin, T Fuhrer, N Zamboni, U Sauer - Nature methods, 2017 - nature.com
Our understanding of metabolism is limited by a lack of knowledge about the functions of
many enzymes. Here, we develop a high-throughput mass spectrometry approach to …

A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives

J Hafner, J Payne, H MohammadiPeyhani… - Nature …, 2021 - nature.com
Plant natural products (PNPs) and their derivatives are important but underexplored sources
of pharmaceutical molecules. To access this untapped potential, the reconstitution of …

Profiling the orphan enzymes

M Sorokina, M Stam, C Médigue, O Lespinet… - Biology direct, 2014 - Springer
Abstract The emergence of Next Generation Sequencing generates an incredible amount of
sequence and great potential for new enzyme discovery. Despite this huge amount of data …

Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites

N Hadadi, H MohammadiPeyhani… - Proceedings of the …, 2019 - National Acad Sciences
Thousands of biochemical reactions with characterized activities are “orphan,” meaning they
cannot be assigned to a specific enzyme, leaving gaps in metabolic pathways. Novel …

Metabolic assessment of E. coli as a Biofactory for commercial products

X Zhang, CJ Tervo, JL Reed - Metabolic engineering, 2016 - Elsevier
Metabolic engineering uses microorganisms to synthesize chemicals from renewable
resources. Given the thousands of known metabolites, it is unclear what valuable chemicals …

Updates in Rhea—a manually curated resource of biochemical reactions

A Morgat, KB Axelsen, T Lombardot… - Nucleic acids …, 2015 - academic.oup.com
Abstract Rhea (http://www. ebi. ac. uk/rhea) is a comprehensive and non-redundant
resource of expert-curated biochemical reactions described using species from the ChEBI …

Exploring biochemical pathways for mono-ethylene glycol (MEG) synthesis from synthesis gas

MA Islam, N Hadadi, M Ataman, V Hatzimanikatis… - Metabolic …, 2017 - Elsevier
Mono-ethylene glycol (MEG) is an important petrochemical with widespread use in
numerous consumer products. The current industrial MEG-production process relies on non …

Mesaconase activity of class I fumarase contributes to mesaconate utilization by Burkholderia xenovorans

M Kronen, J Sasikaran, IA Berg - Applied and environmental …, 2015 - Am Soc Microbiol
Pseudomonas aeruginosa, Yersinia pestis, and many other bacteria are able to utilize the
C5-dicarboxylic acid itaconate (methylenesuccinate). Itaconate degradation starts with its …

Global untargeted serum metabolomic analyses nominate metabolic pathways responsive to loss of expression of the orphan metallo β-lactamase, MBLAC1

CL Gibson, SG Codreanu, AC Schrimpe-Rutledge… - Molecular omics, 2018 - pubs.rsc.org
The C. elegans gene swip-10 encodes an orphan metallo β-lactamase that genetic studies
indicate is vital for limiting neuronal excitability and viability. Sequence analysis indicates …