Predicted structural proteome of Sphagnum divinum and proteome-scale annotation

Davidson, Russell B.; Coletti, Mark; Gao, Mu; Piatkowski, Bryan; Sreedasyam, Avinash; Quadir, Farhan; Weston, David J.; Schmutz, Jeremy; Cheng, Jianlin; Skolnick, Jeffrey; Parks, Jerry M.; Sedova, Ada

doi:10.1093/bioinformatics/btad511

Predicted structural proteome of Sphagnum divinum and proteome-scale annotation

Journal Article · Thu Aug 17 00:00:00 EDT 2023 · Bioinformatics

DOI:https://doi.org/10.1093/bioinformatics/btad511· OSTI ID:1997742

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Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Georgia Institute of Technology, Atlanta, GA (United States)
HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
Univ. of Missouri, Columbia, MO (United States)
HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sphagnum-dominated peatlands store a substantial amount of terrestrial carbon. The genus is undersampled and under-studied. No experimental crystal structure from any Sphagnum species exists in the Protein Data Bank and fewer than 200 Sphagnum-related genes have structural models available in the AlphaFold Protein Structure Database. Tools and resources are needed to help bridge these gaps, and to enable the analysis of other structural proteomes now made possible by accurate structure prediction. We present the predicted structural proteome (25,134 primary transcripts) of Sphagnum divinum computed using AlphaFold, structural alignment results of all high-confidence models against an annotated nonredundant crystallographic database of over 90,000 structures, a structure-based classification of putative Enzyme Commission (EC) numbers across this proteome, and the computational method to perform this proteome-scale structure-based annotation.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1997742

Journal Information:: Bioinformatics, Journal Name: Bioinformatics Journal Issue: 8 Vol. 39; ISSN 1367-4803

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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