ArticleNucleic acids research2024
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 19 citations in OpenAlex.
- "Quadrupling" the protein family space with global metagenomics.Nucleic acids research · 2026Article
- Decoding extremophiles: insights from bioinformatics, machine learning, and data-driven approaches.Briefings in bioinformatics · 2026Review
- metagRoot: a comprehensive database of protein families associated with plant root microbiomes.Nucleic acids research · 2026Article
- CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset.NAR genomics and bioinformatics · 2025Article
- Augmenting microbial phylogenomic signal with tailored marker gene sets.Nature communications · 2025Article
- MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis.Nucleic acids research · 2025Article
- Computational Metagenomics: State of the Art.International journal of molecular sciences · 2025Review
- DSSP 4: FAIR annotation of protein secondary structure.Protein science : a publication of the Protein Society · 2025Article
- Annotating the microbial dark matter with HiFi-NN.iScience · 2025Article
- Visualizing metagenomic and metatranscriptomic data: A comprehensive review.Computational and structural biotechnology journal · 2024Review
- A catalog of small proteins from the global microbiome.Nature communications · 2024Article
- Genome-resolved metagenomics: a game changer for microbiome medicine.Experimental & molecular medicine · 2024Review
- The 2024 Nucleic Acids Research database issue and the online molecular biology database collection.Nucleic acids research · 2024Article
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
The Novel Metagenome Protein Families Database (NMPFamsDB) is a database of metagenome- and metatranscriptome-derived protein families, whose members have no hits to proteins of reference genomes or Pfam domains. Each protein family is accompanied by multiple sequence alignments, Hidden Markov Models, taxonomic information, ecosystem and geolocation metadata, sequence and structure predictions, as well as 3D structure models predicted with AlphaFold2. In its current version, NMPFamsDB hosts over 100 000 protein families, each with at least 100 members. The reported protein families significantly expand (more than double) the number of known protein sequence clusters from reference genomes and reveal new insights into their habitat distribution, origins, functions and taxonomy. We expect NMPFamsDB to be a valuable resource for microbial proteome-wide analyses and for further discovery and characterization of novel functions. NMPFamsDB is publicly available in http://www.nmpfamsdb.org/ or https://bib.fleming.gr/NMPFamsDB.
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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.