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A most wanted list of conserved protein families with no known domains

Stacia K. Wyman, Aram Avila-Herrera, Stephen Nayfach, Katherine S. Pollard
doi: https://doi.org/10.1101/207985
Stacia K. Wyman
1Gladstone Institutes, San Francisco, CA
2University of California, Berkeley, CA
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Aram Avila-Herrera
1Gladstone Institutes, San Francisco, CA
3Lawrence Livermore National Laboratory, Livermore, CA
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Stephen Nayfach
1Gladstone Institutes, San Francisco, CA
4University of California, San Francisco, CA
5DOE Joint Genome Institute, Walnut Creek, CA
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Katherine S. Pollard
1Gladstone Institutes, San Francisco, CA
4University of California, San Francisco, CA
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  • For correspondence: kpollard@gladstone.ucsf.edu
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Abstract

The number and proportion of genes with no known function are growing rapidly. To quantify this phenomenon and provide criteria for prioritizing genes for functional characterization, we developed a bioinformatics pipeline that identifies robustly defined protein families with no annotated domains, ranks these with respect to phylogenetic breadth, and identifies them in metagenomics data. We applied this approach to 271 965 protein families from the SFams database and discovered many with no functional annotation, including >118 000 families lacking any known protein domain. From these, we prioritized 6 668 conserved protein families with at least three sequences from organisms in at least two distinct classes. These Function Unknown Families (FUnkFams) are present in Tara Oceans Expedition and Human Microbiome Project metagenomes, with distributions associated with sampling environment. Our findings highlight the extent of functional novelty in sequence databases and establish an approach for creating a “most wanted” list of genes to characterize.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 23, 2017.
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A most wanted list of conserved protein families with no known domains
Stacia K. Wyman, Aram Avila-Herrera, Stephen Nayfach, Katherine S. Pollard
bioRxiv 207985; doi: https://doi.org/10.1101/207985
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A most wanted list of conserved protein families with no known domains
Stacia K. Wyman, Aram Avila-Herrera, Stephen Nayfach, Katherine S. Pollard
bioRxiv 207985; doi: https://doi.org/10.1101/207985

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