Visualizing the superfamily of metallo-β-lactamases through sequence similarity network neighborhood connectivity analysis
Copyright policy )Visualizing the superfamily of metallo-β-lactamases through sequence similarity network neighborhood connectivity analysis
ABSTRACTThe superfamily of metallo-β-lactamases (MBL) comprises an ancient group of proteins found in all domains of life, sharing a characteristic αββα fold and a histidine-rich motif for binding of transition metal ions, with the ability to catalyze a variety of hydrolysis and redox reactions. Herein, structural homology and sequence similarity network (SSN) analysis are used to assist the phylogenetic reconstruction of the MBL superfamily, introducing tanglegrams to evaluate structure-function relationships. SSN neighborhood connectivity is applied for spotting protein families within SSN clusters, showing that 98 % of the superfamily remains to be explored experimentally. Further SSN research is suggested in order to determine their topological properties, which will be instrumental for the improvement of automated sequence annotation methods.
FOS: Computer and information sciences, Artificial intelligence, Science (General), Protein family, Protein-Protein Interaction Networks, Evolutionary biology, Gene, Computational biology, Q1-390, Engineering, Sequence alignment, https://purl.org/becyt/ford/1.6, NEIGHBORHOOD CONNECTIVITY, Similarity (geometry), Metallo-lactamase, METALLO-LACTAMASE, Sequence analysis, Life Sciences, SUPERFAMILY, Analysis of Gene Interaction Networks, Social sciences (General), Subcellular Localization, Network analysis, Research Article, Interconnectivity, Bioinformatics, Annotation, Gene Set Enrichment Analysis, SEQUENCE SIMILARITY NETWORK, Biochemistry, Genetics and Molecular Biology, Support Vector Machines, Genetics, Peptide sequence, Image (mathematics), Protein sequencing, https://purl.org/becyt/ford/1, Molecular Biology, Biology, H1-99, Prediction of Protein Subcellular Localization, Protein Structure Prediction and Analysis, Protein superfamily, Computer science, Tanglegram, PROTEIN SUPERFAMILY, FOS: Biological sciences, Electrical engineering, TANGLEGRAM, Neighborhood connectivity, Sequence similarity network, Phylogenetic tree, Sequence (biology)
FOS: Computer and information sciences, Artificial intelligence, Science (General), Protein family, Protein-Protein Interaction Networks, Evolutionary biology, Gene, Computational biology, Q1-390, Engineering, Sequence alignment, https://purl.org/becyt/ford/1.6, NEIGHBORHOOD CONNECTIVITY, Similarity (geometry), Metallo-lactamase, METALLO-LACTAMASE, Sequence analysis, Life Sciences, SUPERFAMILY, Analysis of Gene Interaction Networks, Social sciences (General), Subcellular Localization, Network analysis, Research Article, Interconnectivity, Bioinformatics, Annotation, Gene Set Enrichment Analysis, SEQUENCE SIMILARITY NETWORK, Biochemistry, Genetics and Molecular Biology, Support Vector Machines, Genetics, Peptide sequence, Image (mathematics), Protein sequencing, https://purl.org/becyt/ford/1, Molecular Biology, Biology, H1-99, Prediction of Protein Subcellular Localization, Protein Structure Prediction and Analysis, Protein superfamily, Computer science, Tanglegram, PROTEIN SUPERFAMILY, FOS: Biological sciences, Electrical engineering, TANGLEGRAM, Neighborhood connectivity, Sequence similarity network, Phylogenetic tree, Sequence (biology)
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