Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families.

ABSTRACT:

Introduction

The ocean microbiome represents one of the largest microbiomes and produces nearly half of the primary energy on the planet through photosynthesis or chemosynthesis. Using recent advances in marine genomics, we explore new applications of oceanic metagenomes for protein structure and function prediction.

Results

By processing 1.3 TB of high-quality reads from the Tara Oceans data, we obtain 97 million non-redundant genes. Of the 5721 Pfam families that lack experimental structures, 2801 have at least one member associated with the oceanic metagenomics dataset. We apply C-QUARK, a deep-learning contact-guided ab initio structure prediction pipeline, to model 27 families, where 20 are predicted to have a reliable fold with estimated template modeling score (TM-sco

SUBMITTER: Wang Y 

PROVIDER: S-EPMC6825341 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature