Quantitative assessment of protein function prediction from metagenomics shotgun sequences

To assess the potential of protein function prediction in environmental genomics data, we analyzed shotgun sequences from four diverse and complex habitats. Using homology searches as well as customized gene neighborhood methods that incorporate intergenic and evolutionary distances, we inferred spe...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2007-08, Vol.104 (35), p.13913-13918
Main Authors: Harrington, E.D, Singh, A.H, Doerks, T, Letunic, I, von Mering, C, Jensen, L.J, Raes, J, Bork, P
Format: Article
Language:English
Subjects:
Animals
Biochemistry
Biofilms
Biological Sciences
Biosynthesis
Cogs
Databases, Factual
Datasets
Fatty acids
Genes
Genetic Variation
Genome
Genome, Bacterial
Genomes
Genomic Library
Genomics
Hemoglobin
Metagenomics
Models, Genetic
Open Reading Frames
Proteins
Proteins - genetics
Proteins - metabolism
Sea water
Sequence Homology, Amino Acid
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Summary:To assess the potential of protein function prediction in environmental genomics data, we analyzed shotgun sequences from four diverse and complex habitats. Using homology searches as well as customized gene neighborhood methods that incorporate intergenic and evolutionary distances, we inferred specific functions for 76% of the 1.4 million predicted ORFs in these samples (83% when nonspecific functions are considered). Surprisingly, these fractions are only slightly smaller than the corresponding ones in completely sequenced genomes (83% and 86%, respectively, by using the same methodology) and considerably higher than previously thought. For as many as 75,448 ORFs (5% of the total), only neighborhood methods can assign functions, illustrated here by a previously undescribed gene associated with the well characterized heme biosynthesis operon and a potential transcription factor that might regulate a coupling between fatty acid biosynthesis and degradation. Our results further suggest that, although functions can be inferred for most proteins on earth, many functions remain to be discovered in numerous small, rare protein families.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0702636104