ArticleNucleic acids research2025
Domainator, a flexible software suite for domain-based annotation and neighborhood analysis, identifies proteins involved in antiviral systems.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Antiviral defence is a conserved function of diverse bacterial DNA glycosylases.Nature microbiology · 2026Article
- Article
- END nucleases are antiphage defence systems targeting multiple phages with modified genomes.Nature microbiology · 2026Article
- Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.Nucleic acids research · 2026Article
- Uncovering ParB-dependent and -independent subclasses of T-dioxygenases from bacteriophage.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- KlebPhaCol: a community-driven resource for Klebsiella research identified a novel phage family.Nucleic acids research · 2025Article
- Comprehensive nucleoside analysis of archaeal RNA modification profiles reveals an mCell reports · 2025Article
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Authors and funding
8 authors.
Funding
Abstract
The availability of large databases of biological sequences presents an opportunity for in-depth exploration of gene diversity and function. Bacterial defense systems are a rich source of diverse but difficult to annotate genes with biotechnological applications. In this work, we present Domainator, a flexible and modular software suite for domain-based gene neighborhood and protein search, extraction and clustering. We demonstrate the utility of Domainator through three examples related to bacterial defense systems. First, we cluster CRISPR-associated Rossman fold (CARF) containing proteins with difficult to annotate effector domains, classifying most of them as likely transcriptional regulators and a subset as likely RNases. Second, we extract and cluster P4-like phage satellite defense hotspots, identify an abundant variant of Lamassu defense systems and demonstrate its in vivo activity against several T-even phages. Third, we integrate a protein language model into Domainator and use it to identify restriction endonucleases with low similarity to known reference sequences, validating the activity of one example in vitro. Domainator is made available as an open-source package with detailed documentation and usage examples.
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