ArticleHeliyon2021
Visualizing the superfamily of metallo-β-lactamases through sequence similarity network neighborhood connectivity analysis.
Article in Heliyon, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 41 citations in OpenAlex.
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- Molecular interplay between ComEC domains allows for selective degradation of the non-translocating strand during natural transformation.Nucleic acids research · 2025Article
- Disentangling abiotic and biotic effects of treated wastewater on stream biofilm resistomes enables the discovery of a new planctomycete beta-lactamase.Microbiome · 2024Article
- Investigating diversity and similarity between CBM13 modules and ricin-B lectin domains using sequence similarity networks.BMC genomics · 2024Article
- The Structural Biology of Catalase Evolution.Sub-cellular biochemistry · 2024Review
- Class III hybrid cluster protein homodimeric architecture shows evolutionary relationship with Ni, Fe-carbon monoxide dehydrogenases.Nature communications · 2023Article
- Deploying solid-phase synthesis to access thymine-containing nucleoside analogs that inhibit DNA repair nuclease SNM1A.Organic & biomolecular chemistry · 2023Article
- EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools.Journal of molecular biology · 2023Article
- Metal Nanomaterials and Hydrolytic Enzyme-Based Formulations for Improved Antifungal Activity.International journal of molecular sciences · 2023Review
- Recently evolved combination of unique sulfatase and amidase genes enables bacterial degradation of the wastewater micropollutant acesulfame worldwide.Frontiers in microbiology · 2023Article
- Article
- The structure of Synechococcus elongatus enolase reveals key aspects of phosphoenolpyruvate binding.Acta crystallographica. Section F, Structural biology communications · 2022Article
- Dual Activity BLEG-1 fromInternational journal of molecular sciences · 2021Article
- Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design.Chemical reviews · 2021Review
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein sequence similarity networks (SSNs) constitute a convenient approach to analyze large polypeptide sequence datasets, and have been successfully applied to study a number of protein families over the past decade. SSN analysis is herein combined with traditional cladistic and phenetic phylogenetic analysis (respectively based on multiple sequence alignments and all-against-all three-dimensional protein structure comparisons) in order to assist the ancestral reconstruction and integrative revision of the superfamily of metallo-β-lactamases (MBLs). It is shown that only 198 out of 15,292 representative nodes contain at least one experimentally obtained protein structure in the Protein Data Bank or a manually annotated SwissProt entry, that is to say, only 1.3 % of the superfamily has been functionally and/or structurally characterized. Besides, neighborhood connectivity coloring, which measures local network interconnectivity, is introduced for detection of protein families within SSN clusters. This approach provides a clear picture of how many families remain unexplored in the superfamily, while most MBL research is heavily biased towards a few families. Further research is suggested in order to determine the SSN topological properties, which will be instrumental for the improvement of automated sequence annotation methods.
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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.