title: Protein function space: viewing the limits or limited by our view?
abstract: Given that the number of protein functions on earth is finite, the rapid expansion of biological knowledge and the concomitant exponential increase in the number of protein sequences should, at some point, enable the estimation of the limits of protein function space. The functional coverage of protein sequences can be investigated using computational methods, especially given the massive amount of data being generated by large-scale environmental sequencing (metagenomics). In completely sequenced genomes, the fraction of proteins to which at least some functional features can be assigned has recently risen to as much as approximately 85%. Although this fraction is more uncertain in metagenomics surveys, because of environmental complexities and differences in analysis protocols, our global knowledge of protein functions still appears to be considerable. However, when we consider protein families, continued sequencing seems to yield an ever-increasing number of novel families. Until we reconcile these two views, the limits of protein space will remain obscured.
authors.affiliation: European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
authors.forename: Jeroen
authors.initials: J
authors.lastname: Raes
authors.forename: Eoghan Donal
authors.initials: ED
authors.lastname: Harrington
authors.forename: Amoolya Hardev
authors.initials: AH
authors.lastname: Singh
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
mesh_terms: D000818:Animals; D001671:Biochemistry / Q000639:trends*; D004926:Escherichia coli / Q000502:physiology; D006801:Humans; D011506:Proteins / Q000235:genetics / Q000502:physiology*; D020539:Sequence Analysis, Protein
chemical_list: D011506:Proteins