ArticleFrontiers in microbiology2019
Whole Proteome Clustering of 2,307 Proteobacterial Genomes Reveals Conserved Proteins and Significant Annotation Issues.
Article in Frontiers in microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 9 citations in OpenAlex.
- Limitations of current machine learning models in predicting enzymatic functions for uncharacterized proteins.G3 (Bethesda, Md.) · 2025Article
- Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy.PloS one · 2021Article
- PASS: Protein Annotation Surveillance Site for Protein Annotation Using Homologous Clusters, NLP, and Sequence Similarity Networks.Frontiers in bioinformatics · 2021Article
- A Need for Improved Cellulase Identification from Metagenomic Sequence Data.Applied and environmental microbiology · 2020Article
- Assessment of a Potential Role ofFrontiers in microbiology · 2020Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
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Abstract
We clustered 8.76 M protein sequences deduced from 2,307 completely sequenced Proteobacterial genomes resulting in 707,311 clusters of one or more sequences of which 224,442 ranged in size from 2 to 2,894 sequences. To our knowledge this is the first study of this scale. We were surprised to find that no single cluster contained a representative sequence from all the organisms in the study. Given the minimal genome concept, we expected to find a shared set of proteins. To determine why the clusters did not have universal representation we chose four essential proteins, the chaperonin GroEL, DNA dependent RNA polymerase subunits beta and beta' (RpoB/RpoB'), and DNA polymerase I (PolA), representing fundamental cellular functions, and examined their cluster distribution. We found these proteins to be remarkably conserved with certain caveats. Although the
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