ArticlemSystems2020
GapMind: Automated Annotation of Amino Acid Biosynthesis.
Article in mSystems, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed, 80 citations in OpenAlex.
- Low Levels of Amino Acid Auxotrophy Among Environmental Pseudomonas Isolates.Environmental microbiology · 2026Article
- Cross-feeding enables robust coexistence between four bacterial species.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A syntenic pangenome of Gardnerella reveals novel plasmids and phage, taxonomic boundaries, and species-level stratification of metabolic and virulence potential.Nature communications · 2026Article
- Effects of Roughage Combinations of Sugarcane Dry Leaves and Peanut Vine on the Rumen Microbial Community and Metabolites of Weaned Buffalo Calves.Microorganisms · 2026Article
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- Infant gut microbiomes contribute to metabolic states that impact brain function.bioRxiv : the preprint server for biology · 2026Article
- Predator avoidance promotes inter-bacterial symbiosis with myxobacteria in polymicrobial communities.bioRxiv : the preprint server for biology · 2026Article
- Genomic and phenotypic characterization of a human gutFuture microbiology · 2026Article
- Induced pathogenicity toward open-ocean diatoms by a filterable bacterium Ekhidna algicida sp. nov.The ISME journal · 2026Article
- Predator avoidance promotes interbacterial symbiosis with myxobacteria in polymicrobial communities.The ISME journal · 2026Article
- Microbially derived essential amino acids compensate for dietary deficiencies in an ecologically relevant mammalian host.The ISME journal · 2026Article
- Microbial model communities exhibit widespread metabolic interdependencies.Communications biology · 2025Article
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- Cobamide-based interactions between soil bacteria can be predicted based on monoculture growth.bioRxiv : the preprint server for biology · 2025Article
- Integrative microbiome- and metatranscriptome-based analyses reveal diagnostic biomarkers for peri-implantitis.NPJ biofilms and microbiomes · 2025Article
- Microbial diversity and functional potential of the Halobates melleus (Heteroptera: Gerridae) microbiome from the Red Sea coastline.Environmental microbiome · 2025Article
- Genetic Drivers of Plant Root Colonisation by the Biocontrol Agent Pseudomonas protegens Pf-5.Environmental microbiology reports · 2025Article
- Disruption-induced changes in syntrophic propionate and acetate oxidation: flocculation, cell proximity, and microbial activity.Biotechnology for biofuels and bioproducts · 2025Article
- Article
- Bacterial Amino Acid Auxotrophies Enable Energetically Costlier Proteomes.International journal of molecular sciences · 2025Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
GapMind is a Web-based tool for annotating amino acid biosynthesis in bacteria and archaea (http://papers.genomics.lbl.gov/gaps). GapMind incorporates many variant pathways and 130 different reactions, and it analyzes a genome in just 15 s. To avoid error-prone transitive annotations, GapMind relies primarily on a database of experimentally characterized proteins. GapMind correctly handles fusion proteins and split proteins, which often cause errors for best-hit approaches. To improve GapMind's coverage, we examined genetic data from 35 bacteria that grow in defined media without amino acids, and we filled many gaps in amino acid biosynthesis pathways. For example, we identified additional genes for arginine synthesis with succinylated intermediates in
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Registered trials
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.