DH{}DataHunter

Dataset from Zenodo · Srouji, John

The Evolution of Function within the Nudix Superfamily

Open on Zenodo
License
CC BY 4.0commercial use allowedLicense text
This license allows commercial use. Usually you must credit the author; read the license for the exact terms.
Formats
PY, R, CSV, FA, NEWICK, DOC
Size
140 MB
Updated
Jul 19, 2024

Description

The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 "select" Nudix domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based…

Description from Zenodo, shortened.

Files (28)

  • PY3DCOMB_alignment.py8.1 MB
  • Rgenerate_score_biochem_genetic.R892 byte
  • CSVscore_biochem_genetic_soverall.csv40 kB
  • FA78-PDB_alignment.fa32 kB
  • Rgenerate_score_final.R1.3 kB
  • CSVscore_final.csv99 kB
  • NEWICKNudix-clan_tree.newick1.4 MB
  • CSVscore_genetic.csv1.5 kB
  • DOCTable S1 updated.doc72 kB
  • CSVscore_biochem_genetic.csv40 kB
  • PDFThe_layout_of_the_Nudix_MySQL_database.pdf282 kB
  • DENDRO347-select_tree_reconciled.dendro101 kB
  • FANudix-clan_alignment.fa108 MB
  • FA46-PDB_alignment.fa40 kB
  • XLSXNudix_data_collection.xlsx204 kB
  • SQLmysql_dump_char_nudix_04062014.sql880 kB
  • PDFFigure_7_347-select_tree_high_resolution.pdf978 kB
  • PDFFigure_8_Nudix-clan_tree_high_resolution.pdf1.8 MB
  • PDFPipelines_to_build_sequence_alignments_of_the_Nudix_superfamily.pdf1.6 MB
  • XLSXFinal_score_assignment.xlsx167 kB
  • XLSXGOA_analysis_results.xlsx5.5 MB
  • NEWICK347-select_tree.newick14 kB
  • CSVscore_biochem.csv68 kB
  • FA347-select_alignment.fa183 kB
  • XLSX340_select_nudix_proteins.xlsx50 kB
  • FA324-core_alignment.fa158 kB
  • XLSXInitial_score_assignment.xlsx173 kB
  • DENDRONudix-clan_tree_reconciled.dendro10 MB

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