ArticleNucleic acids research2024
dbAPIS: a database of anti-prokaryotic immune system genes.
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 31 papers.
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Who cites it
31 citing papers in PubMed, 41 citations in OpenAlex.
- An expanded realm of anti-CRISPR-associated proteins and regulatory mechanisms.Nucleic acids research · 2026Article
- Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.Nucleic acids research · 2026Article
- Review
- Analysis of a Novel T1-like Phage KanT1 Reveals a Standalone SH3 Domain as a Widespread Component ofInternational journal of molecular sciences · 2026Article
- Plasmids as persistent genetic reservoirs of bacterial defense systems in wastewater treatment.Microbiome · 2026Article
- Co-occurrence of diverse defense systems shapes complex microbe-virus relationships in deep-sea cold seeps.Nature communications · 2026Article
- CRISPR spacer profiling and prophage mining reveal diverse bacteriophages associated withJournal of oral microbiology · 2026Article
- Staphylococcal phages as agents of evolution and innovation: From gene flow to next-generation therapeutics.Genetics and molecular biology · 2026Article
- Unraveling the diversity, function, and virus-host interactions of archaeal proviruses.ISME communications · 2026Article
- A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions.bioRxiv : the preprint server for biology · 2025Article
- In silico approaches for discovering microbial antiviral defense systems.Briefings in bioinformatics · 2025Review
- The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes.Science advances · 2025Article
- Strengthening phage resistance of Streptococcus thermophilus by leveraging complementary defense systems.Nature communications · 2025Article
- The extended mobility of plasmids.Nucleic acids research · 2025Review
- The Arms Race Between Actinobacillus pleuropneumoniae and Its Genetic Environment: A Comprehensive Analysis of Its Defensome and Mobile Genetic Elements.Molecular microbiology · 2025Article
- Interactions and evolutionary relationships among bacterial mobile genetic elements.Nature reviews. Microbiology · 2025Review
- AcrDB update: Predicted 3D structures of anti-CRISPRs in human gut viromes.Protein science : a publication of the Protein Society · 2025Article
- Article
- LoVis4u: a locus visualization tool for comparative genomics and coverage profiles.NAR genomics and bioinformatics · 2025Article
- Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer.Genome research · 2025Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Anti-prokaryotic immune system (APIS) proteins, typically encoded by phages, prophages, and plasmids, inhibit prokaryotic immune systems (e.g. restriction modification, toxin-antitoxin, CRISPR-Cas). A growing number of APIS genes have been characterized and dispersed in the literature. Here we developed dbAPIS (https://bcb.unl.edu/dbAPIS), as the first literature curated data repository for experimentally verified APIS genes and their associated protein families. The key features of dbAPIS include: (i) experimentally verified APIS genes with their protein sequences, functional annotation, PDB or AlphaFold predicted structures, genomic context, sequence and structural homologs from different microbiome/virome databases; (ii) classification of APIS proteins into sequence-based families and construction of hidden Markov models (HMMs); (iii) user-friendly web interface for data browsing by the inhibited immune system types or by the hosts, and functions for searching and batch downloading of pre-computed data; (iv) Inclusion of all types of APIS proteins (except for anti-CRISPRs) that inhibit a variety of prokaryotic defense systems (e.g. RM, TA, CBASS, Thoeris, Gabija). The current release of dbAPIS contains 41 verified APIS proteins and ∼4400 sequence homologs of 92 families and 38 clans. dbAPIS will facilitate the discovery of novel anti-defense genes and genomic islands in phages, by providing a user-friendly data repository and a web resource for an easy homology search against known APIS proteins.
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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.