ReviewComputational and structural biotechnology journal2014
Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway.
Review in Computational and structural biotechnology journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 39 citations in OpenAlex.
- Isolation of genome-predicted Caldatribacterium (Atribacterota) reveals pervasive microbial cultivation problem due to folate precipitation.Nature communications · 2026Article
- How mutagenesis and laboratory conditions affect the genome of the metal-resistant bacteriumJournal of bacteriology · 2026Article
- Limitations of current machine learning models in predicting enzymatic functions for uncharacterized proteins.G3 (Bethesda, Md.) · 2025Article
- Multisubstrate specificity shaped the complex evolution of the aminotransferase family across the tree of life.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Microenzymes: Is There Anybody Out There?The protein journal · 2024Review
- Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages.Microbiology and molecular biology reviews : MMBR · 2024Review
- In Silico Safety Assessment ofInternational journal of molecular sciences · 2024Article
- Taxonomic and environmental distribution of bacterial amino acid auxotrophies.Nature communications · 2023Article
- Diversification of Ubiquinone Biosynthesis via Gene Duplications, Transfers, Losses, and Parallel Evolution.Molecular biology and evolution · 2023Article
- Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes.Microbial genomics · 2023Article
- Coevolution of Metabolic Pathways in Blattodea and TheirMicrobiology spectrum · 2022Article
- A roadmap for the functional annotation of protein families: a community perspective.Database : the journal of biological databases and curation · 2022Article
- Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase.Biomolecules · 2021Article
- Open Issues for Protein Function Assignment inGenes · 2021Article
- Multi-Omics Characterization of Host-DerivedFrontiers in microbiology · 2021Article
- An Unusual Route forJournal of bacteriology · 2020Article
- GapMind: Automated Annotation of Amino Acid Biosynthesis.mSystems · 2020Article
- Composite genome sequence of Bacillus clausii, a probiotic commercially available as EnterogerminaBMC microbiology · 2019Article
- The uridylyltransferase GlnD and tRNA modification GTPase MnmE allosterically controlThe Journal of biological chemistry · 2018Article
- Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics.PLoS genetics · 2018Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The availability of thousands of sequenced genomes has revealed the diversity of biochemical solutions to similar chemical problems. Even for molecules at the heart of metabolism, such as cofactors, the pathway enzymes first discovered in model organisms like Escherichia coli or Saccharomyces cerevisiae are often not universally conserved. Tetrahydrofolate (THF) (or its close relative tetrahydromethanopterin) is a universal and essential C1-carrier that most microbes and plants synthesize de novo. The THF biosynthesis pathway and enzymes are, however, not universal and alternate solutions are found for most steps, making this pathway a challenge to annotate automatically in many genomes. Comparing THF pathway reconstructions and functional annotations of a chosen set of folate synthesis genes in specific prokaryotes revealed the strengths and weaknesses of different microbial annotation platforms. This analysis revealed that most current platforms fail in metabolic reconstruction of variant pathways. However, all the pieces are in place to quickly correct these deficiencies if the different databases were built on each other's strengths.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.