CoChat
Sign Up
Cited by 10Genomics and Phylogenetic StudiesCRISPR and Genetic EngineeringBacteriophages and microbial interactions

The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.

Domainator, a flexible software suite for domain-based annotation and neighborhood analysis, identifies proteins involved in antiviral systems

Open access
Johnson, Sean R, Weigele, Peter R, Fomenkov, Alexey, Ge, Andrew, Vincze, Anna, Eaglesham, James B, Roberts, Richard J, Sun, Zhiyi·2025·Nucleic Acids Research
DOI 10.1093/nar/gkae1175PMC PMC11754643

Published version of a preprint

Open this paper in CoChat — free accountOpen PDF

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.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1093/nar/gkae1175

Cites

6 of 6 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 77

  1. De Crécy-Lagard, 2022, A roadmap for the functional annotation of protein families: a community perspective, Database, 2022, baac062, 10.1093/database/baac062 · DOI
  2. Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389, 10.1093/nar/25.17.3389 · DOI · Paper page
  3. Devos, 2001, Intrinsic errors in genome annotation, Trends Genet., 17, 429, 10.1016/S0168-9525(01)02348-4 · DOI
  4. Eddy, 2011, Accelerated profile HMM searches, PLOS Comput. Biol., 7, e1002195, 10.1371/journal.pcbi.1002195 · DOI · Paper page
  5. Mistry, 2021, Pfam: the protein families database in 2021, Nucleic Acids Res., 49, D412, 10.1093/nar/gkaa913 · DOI · Paper page
  6. Aramaki, 2020, KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold, Bioinformatics, 36, 2251, 10.1093/bioinformatics/btz859 · DOI · Paper page
  7. Cantarel, 2009, The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics, Nucleic Acids Res., 37, D233, 10.1093/nar/gkn663 · DOI
  8. Tatusova, 2016, NCBI prokaryotic genome annotation pipeline, Nucleic Acids Res., 44, 6614, 10.1093/nar/gkw569 · DOI
  9. Ruhe, 2020, Polymorphic toxins and their immunity proteins: diversity, evolution, and mechanisms of delivery, Annu. Rev. Microbiol., 74, 497, 10.1146/annurev-micro-020518-115638 · DOI
  10. Lutz, 2019, A protein architecture guided screen for modification dependent restriction endonucleases, Nucleic Acids Res., 47, 9761, 10.1093/nar/gkz755 · DOI
  11. Gilchrist, 2021, cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters, Bioinforma. Adv., 1, vbab016, 10.1093/bioadv/vbab016 · DOI
  12. Oberg, 2023, EFI-EST, EFI-GNT, and EFI-CGFP: enzyme Function Initiative (EFI) web resource for Genomic enzymology tools, J. Mol. Biol., 435, 168018, 10.1016/j.jmb.2023.168018 · DOI
  13. Blin, 2021, antiSMASH 6.0: improving cluster detection and comparison capabilities, Nucleic Acids Res., 49, W29, 10.1093/nar/gkab335 · DOI
  14. Mariano, 2019, A family of type VI secretion system effector proteins that form ion-selective pores, Nat. Commun., 10, 5484, 10.1038/s41467-019-13439-0 · DOI
  15. Snel, 2000, STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene, Nucleic Acids Res., 28, 3442, 10.1093/nar/28.18.3442 · DOI
  16. Szklarczyk, 2023, The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest, Nucleic Acids Res., 51, D638, 10.1093/nar/gkac1000 · DOI · Paper page
  17. Dehal, 2010, MicrobesOnline: an integrated portal for comparative and functional genomics, Nucleic Acids Res., 38, D396, 10.1093/nar/gkp919 · DOI
  18. Kanehisa, 2000, KEGG: kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Res., 28, 27, 10.1093/nar/28.1.27 · DOI · Paper page
  19. Karp, 2019, The BioCyc collection of microbial genomes and metabolic pathways, Brief. Bioinform., 20, 1085, 10.1093/bib/bbx085 · DOI
  20. Makarova, 2011, Defense islands in bacterial and archaeal genomes and prediction of novel defense systems, J. Bacteriol., 193, 6039, 10.1128/JB.05535-11 · DOI
  21. Sibley, 2004, Cassette-like variation of restriction enzyme genes in Escherichia coli C and relatives, Nucleic Acids Res., 32, 522, 10.1093/nar/gkh194 · DOI
  22. Rousset, 2022, Phages and their satellites encode hotspots of antiviral systems, Cell Host Microbe., 30, 740, 10.1016/j.chom.2022.02.018 · DOI
  23. Remmert, 2012, HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment, Nat. Methods, 9, 173, 10.1038/nmeth.1818 · DOI · Paper page
  24. Holm, 2022, Dali server: structural unification of protein families, Nucleic Acids Res., 50, W210, 10.1093/nar/gkac387 · DOI
  25. Varadi, 2022, AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models, Nucleic Acids Res., 50, D439, 10.1093/nar/gkab1061 · DOI · Paper page
  26. Ayoub, 2019, RUPEE: a fast and accurate purely geometric protein structure search, PLoS One, 14, e0213712, 10.1371/journal.pone.0213712 · DOI
  27. Edgar, 2024, Protein structure alignment by reseek improves sensitivity to remote homologs, Bioinformatics, 40, btae687, 10.1093/bioinformatics/btae687 · DOI
  28. Heinzinger, 2024, Bilingual language model for protein sequence and structure, NAR genom. bioinform., 6, lqae150, 10.1093/nargab/lqae150 · DOI · Paper page
  29. Johnson, 2024, Sensitive remote homology search by local alignment of small positional embeddings from protein language models, eLife, 12, RP91415, 10.7554/eLife.91415 · DOI · Paper page
  30. Makarova, 2014, CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems, Front. Genet., 5, 102, 10.3389/fgene.2014.00102 · DOI
  31. Makarova, 2020, Evolutionary and functional classification of the CARF domain superfamily, key sensors in prokaryotic antivirus defense, Nucleic Acids Res., 48, 8828, 10.1093/nar/gkaa635 · DOI
  32. Cock, 2009, Biopython: freely available Python tools for computational molecular biology and bioinformatics, Bioinformatics, 25, 1422, 10.1093/bioinformatics/btp163 · DOI · Paper page
  33. Larralde, 2023, PyHMMER: a Python library binding to HMMER for efficient sequence analysis, Bioinformatics, 39, btad214, 10.1093/bioinformatics/btad214 · DOI
  34. Harris, 2020, Array programming with NumPy, Nature, 585, 357, 10.1038/s41586-020-2649-2 · DOI · Paper page
  35. Virtanen, 2020, SciPy 1.0: fundamental algorithms for scientific computing in Python, Nat. Methods, 17, 261, 10.1038/s41592-019-0686-2 · DOI · Paper page
  36. McKinney, 2010, Data Structures for Statistical Computing in Python, 56, 10.25080/Majora-92bf1922-00a · DOI
  37. Fu, 2012, CD-HIT: accelerated for clustering the next-generation sequencing data, Bioinformatics, 28, 3150, 10.1093/bioinformatics/bts565 · DOI · Paper page
  38. Buchfink, 2021, Sensitive protein alignments at tree-of-life scale using DIAMOND, Nat. Methods, 18, 366, 10.1038/s41592-021-01101-x · DOI · Paper page
  39. Hyatt, 2010, Prodigal: prokaryotic gene recognition and translation initiation site identification, BMC Bioinf., 11, 119, 10.1186/1471-2105-11-119 · DOI
  40. Larralde, 2022, Pyrodigal: python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes, J. Open Source Softw., 7, 4296, 10.21105/joss.04296 · DOI
  41. Waskom, 2021, seaborn: statistical data visualization, J. Open Source Softw., 6, 3021, 10.21105/joss.03021 · DOI · Paper page
  42. McInnes, 2018, UMAP: uniform Manifold approximation and projection, J. Open Source Softw., 3, 861, 10.21105/joss.00861 · DOI · Paper page
  43. Gerlt, 2015, Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): a web tool for generating protein sequence similarity networks, Biochim. Biophys. Acta BBA - Proteins Proteomics, 1854, 1019, 10.1016/j.bbapap.2015.04.015 · DOI
  44. Lin, 2006, An initial strategy for comparing proteins at the domain architecture level, Bioinformatics, 22, 2081, 10.1093/bioinformatics/btl366 · DOI
  45. Navarro-Muñoz, 2020, A computational framework to explore large-scale biosynthetic diversity from large-scale genomic data, Nat. Chem. Biol., 16, 60, 10.1038/s41589-019-0400-9 · DOI
  46. Söding, 2005, Protein homology detection by HMM–HMM comparison, Bioinformatics, 21, 951, 10.1093/bioinformatics/bti125 · DOI
  47. Steinegger, 2019, HH-suite3 for fast remote homology detection and deep protein annotation, BMC Bioinf., 20, 473, 10.1186/s12859-019-3019-7 · DOI · Paper page
  48. Shannon, 2003, Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res., 13, 2498, 10.1101/gr.1239303 · DOI · Paper page
  49. Mirdita, 2022, ColabFold: making protein folding accessible to all, Nat. Methods, 19, 679, 10.1038/s41592-022-01488-1 · DOI · Paper page
  50. Kingston, 2015, Novel recA-independent horizontal gene transfer in Escherichia coli K-12, PLoS One, 10, e0130813, 10.1371/journal.pone.0130813 · DOI
  51. Pryor, 2022, Rapid 40 kb genome construction from 52 parts through data-optimized assembly design, ACS Synth. Biol., 11, 2036, 10.1021/acssynbio.1c00525 · DOI
  52. Bonilla, 2018, Phage on tap: a quick and efficient protocol for the preparation of bacteriophage laboratory stocks, Methods Mol. Biol. Clifton NJ, 1838, 37, 10.1007/978-1-4939-8682-8_4 · DOI
  53. Gao, 2020, Diverse enzymatic activities mediate antiviral immunity in prokaryotes, Science, 369, 1077, 10.1126/science.aba0372 · DOI
  54. Zallot, 2019, The EFI web resource for genomic enzymology tools: leveraging protein, genome, and metagenome databases to discover novel enzymes and metabolic pathways, Biochemistry, 58, 4169, 10.1021/acs.biochem.9b00735 · DOI
  55. Néron, 2023, MacSyFinder v2: improved modelling and search engine to identify molecular systems in genomes, Peer Community J., 3, e28, 10.24072/pcjournal.250 · DOI
  56. Sayers, 2020, GenBank, Nucleic Acids Res., 48, D84
  57. Paysan-Lafosse, 2023, InterPro in 2022, Nucleic Acids Res., 51, D418, 10.1093/nar/gkac993 · DOI
  58. Roberts, 2023, REBASE: a database for DNA restriction and modification: enzymes, genes and genomes, Nucleic Acids Res., 51, D629, 10.1093/nar/gkac975 · DOI
  59. Edgar, 2010, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, 26, 2460, 10.1093/bioinformatics/btq461 · DOI
  60. Zhang, 2005, TM-align: a protein structure alignment algorithm based on the TM-score, Nucleic Acids Res., 33, 2302, 10.1093/nar/gki524 · DOI · Paper page
  61. Makarova, 2020, Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants, Nat. Rev. Microbiol., 18, 67, 10.1038/s41579-019-0299-x · DOI · Paper page
  62. Steens, 2022, The diverse arsenal of type III CRISPR–Cas-associated CARF and SAVED effectors, Biochem. Soc. Trans., 50, 1353, 10.1042/BST20220289 · DOI
  63. Stella, 2024, Type III CRISPR-Cas: beyond the Cas10 effector complex, Trends Biochem. Sci., 49, 28, 10.1016/j.tibs.2023.10.006 · DOI
  64. Pillon, 2021, HEPN RNases – An emerging class of functionally distinct RNA processing and degradation enzymes, Crit. Rev. Biochem. Mol. Biol., 56, 88, 10.1080/10409238.2020.1856769 · DOI
  65. Niewoehner, 2016, Structural basis for the endoribonuclease activity of the type III-A CRISPR-associated protein Csm6, RNA, 22, 318, 10.1261/rna.054098.115 · DOI
  66. Kita, 1999, Evidence of horizontal transfer of theEcoO109I restriction-modification gene to Escherichia coli chromosomal DNA, J. Bacteriol., 181, 6822, 10.1128/JB.181.21.6822-6827.1999 · DOI
  67. Doron, 2018, Systematic discovery of antiphage defense systems in the microbial pangenome, Science, 359, eaar4120, 10.1126/science.aar4120 · DOI
  68. Cheng, 2021, A nucleotide-sensing endonuclease from the Gabija bacterial defense system, Nucleic Acids Res., 49, 5216, 10.1093/nar/gkab277 · DOI
  69. Millman, 2022, An expanded arsenal of immune systems that protect bacteria from phages, Cell Host Microbe., 30, 1556, 10.1016/j.chom.2022.09.017 · DOI · Paper page
  70. Jaskólska, 2022, Two defence systems eliminate plasmids from seventh pandemic Vibrio cholerae, Nature, 604, 323, 10.1038/s41586-022-04546-y · DOI
  71. Payne, 2021, Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types, Nucleic Acids Res., 49, 10868, 10.1093/nar/gkab883 · DOI
  72. Loenen, 2014, Highlights of the DNA cutters: a short history of the restriction enzymes, Nucleic Acids Res., 42, 3, 10.1093/nar/gkt990 · DOI
  73. Card, 1990, Cloning and characterization of the HpaII methylase gene, Nucleic Acids Res., 18, 1377, 10.1093/nar/18.6.1377 · DOI
  74. Camacho, 2009, BLAST+: architecture and applications, BMC Bioinf., 10, 421, 10.1186/1471-2105-10-421 · DOI · Paper page
  75. Roberts, 2003, A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes, Nucleic Acids Res., 31, 1805, 10.1093/nar/gkg274 · DOI · Paper page
  76. Zheng, 2023, dbCAN3: automated carbohydrate-active enzyme and substrate annotation, Nucleic Acids Res., 51, W115, 10.1093/nar/gkad328 · DOI
  77. Tesson, 2022, Systematic and quantitative view of the antiviral arsenal of prokaryotes, Nat. Commun., 13, 2561, 10.1038/s41467-022-30269-9 · DOI

Metadata

Authors
Johnson, S. R., Weigele, P. R., Fomenkov, A., Ge, A., Vincze, A., Eaglesham, J. B., Roberts, R. J., & Sun, Z.
Affiliations
New England Biolabs (United States) (US)
Corresponding author
  • Weigele, Peter R
  • Sun, Zhiyi
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2024-12-09
Volume
53
Issue
2
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkae1175
PMC
PMC11754643
OpenAlex
W4405221537
Cited by
10
References
6
Citations by year
2026: 5 · 2025: 4 · 2024: 1
FWCI
1.36
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
Funders
New England Biolabs
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
  • Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
Keywords
protein clustering, bacterial defense mechanisms, effector domain, transcription factors, ribonuclease, restriction enzymes, protein language models, antiviral proteins
MeSH terms
Protein Domains, Bacterial Proteins, Bacteriophages, DNA Restriction Enzymes, Software, Molecular Sequence Annotation, CRISPR-Associated Proteins

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review