ArticleBMC genomics2006
Phylogenomic analysis of the GIY-YIG nuclease superfamily.
Article in BMC genomics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
97 citing papers in PubMed, 128 citations in OpenAlex.
- Article
- A giant virus in a small lake: characterization of a new tropical algal virus expands the geographical and genetic diversity of the Brazilian virosphere.Journal of virology · 2026Article
- Sequence and structural alignments reveal insights into ANKLE2 evolution and function.Protein science : a publication of the Protein Society · 2026Article
- A bacterial defense system targeting modified cytosine of phage genomic DNA.Nature communications · 2026Article
- Modular determinants of cleavage preference in GIY-YIG nucleases revealed by block-based DNA shuffling and directed evolution.Nucleic acids research · 2026Article
- A buffer-tuning strategy to profile domain-specific activity of chimeric I-TevI/CRISPR gene editors in vitro.Scientific reports · 2025Article
- Host-Specific Adaptation of Legionella pneumophila to Single and Multiple Hosts.Molecular biology and evolution · 2025Article
- Lineage-specific expansions of polinton-like viruses in photosynthetic cryptophytes.Microbiome · 2025Article
- Halting Recombinant Adeno-Associated Virus Transgene Expression Using mRNA-Lipid Nanoparticle-Delivered Meganucleases.Human gene therapy · 2025Article
- Functional dissection of the conserved C. elegans LEM-3/ANKLE1 nuclease reveals a crucial requirement for the LEM-like and GIY-YIG domains for DNA bridge processing.Nucleic acids research · 2025Article
- Discovery of the widespread site-specific single-stranded nuclease family Ssn.Nature communications · 2025Article
- Candida albicans PPR proteins are required for the expression of respiratory Complex I subunits.Genetics · 2024Article
- Exploring the structural landscape of DNA maintenance proteins.Nature communications · 2024Article
- Gene Transfer Among Viruses Substantially Contributes to Gene Gain of Giant Viruses.Molecular biology and evolution · 2024Article
- Assembly and Genome Annotation of Different Strains of Apple Fruit Moth Virus (International journal of molecular sciences · 2024Article
- Plant Organellar MSH1 Is a Displacement Loop-Specific Endonuclease.Plant & cell physiology · 2024Article
- A Photoresponsive Homing Endonuclease for Programmed DNA Cleavage.ACS synthetic biology · 2024Article
- Characterization of winged helix domain fusion endonucleases as N6-methyladenine-dependent type IV restriction systems.Frontiers in microbiology · 2024Article
- A Class 4-like Chromosomal Integron Found inMicroorganisms · 2023Article
- Article
37 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundThe GIY-YIG domain was initially identified in homing endonucleases and later in other selfish mobile genetic elements (including restriction enzymes and non-LTR retrotransposons) and in enzymes involved in DNA repair and recombination. However, to date no systematic search for novel members of the GIY-YIG superfamily or comparative analysis of these enzymes has been reported.
resultsWe carried out database searches to identify all members of known GIY-YIG nuclease families. Multiple sequence alignments together with predicted secondary structures of identified families were represented as Hidden Markov Models (HMM) and compared by the HHsearch method to the uncharacterized protein families gathered in the COG, KOG, and PFAM databases. This analysis allowed for extending the GIY-YIG superfamily to include members of COG3680 and a number of proteins not classified in COGs and to predict that these proteins may function as nucleases, potentially involved in DNA recombination and/or repair. Finally, all old and new members of the GIY-YIG superfamily were compared and analyzed to infer the phylogenetic tree.
conclusionAn evolutionary classification of the GIY-YIG superfamily is presented for the very first time, along with the structural annotation of all (sub)families. It provides a comprehensive picture of sequence-structure-function relationships in this superfamily of nucleases, which will help to design experiments to study the mechanism of action of known members (especially the uncharacterized ones) and will facilitate the prediction of function for the newly discovered ones.
Indexed as
Identifiers
What OpenQuestion holds
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.