Downloads for "Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes"

by Morgan N. Price, Kelly M. Wetmore, R. Jordan Waters, Ryan A. Melnyk, Mark Callaghan, Jayashree Ray, Jennifer V. Kuehl, Ryan A. Melnyk, Jacob S. Lamson, Yumi Suh, Zuelma Esquivel, Harini Sadeeshkumar, Romy Chakraborty, Jim Bristow, Matthew J. Blow, Adam A. Arkin, and Adam M. Deutschbauer

Abstract

The function of nearly half of all protein-coding genes identified in bacterial genomes remains unknown. To systematically explore the functions of these proteins, we generated saturated transposon mutant libraries from 25 diverse bacteria and we assayed mutant phenotypes across hundreds of distinct conditions. From 3,903 genome-wide mutant fitness assays, we obtained 14.9 million gene phenotype measurements and we identified a mutant phenotype for 8,487 proteins with previously unknown functions. The majority of these hypothetical proteins (57%) had phenotypes that were either specific to a few conditions or were similar to that of another gene, thus enabling us to make informed predictions of protein function. For 1,914 of these hypothetical proteins, the functional associations are conserved across related proteins from different bacteria, which confirms that these associations are genuine. This comprehensive catalogue of experimentally-annotated protein functions also enables the targeted exploration of specific biological processes. For example, sensitivity to a DNA-damaging agent revealed 28 known families of DNA repair proteins and 11 putative novel families. Across all sequenced bacteria, 14% of proteins that lack detailed annotations have an ortholog with a functional association in our data set. Our study demonstrates the utility and scalability of high-throughput genetics for large-scale annotation of bacterial proteins and provides a vast compendium of experimentally-determined protein functions across diverse bacteria.

See bioRxiv preprint

Data Downloads

The easiest way to view the data is with the Fitness Browser. You can also download the data for each organism here: and information about the organisms and their genomes:

The gene annotations that we used (from NCBI, IMG, or RAST) are available from the organism-specific web sites and are not included in the protein sequences download.

Also note that for some organisms, the Fitness Browser contains additional experiments beyond those described here. For these organisms, the cofitness values will not match.

Other Downloads

Page by Morgan N. Price, Arkin group, August 2016