title: DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe.
abstract: BACKGROUND
  Computational predictions of catalytic function are vital for in-depth understanding of enzymes. Because several novel approaches performing better than the common BLAST tool are rarely applied in research, we hypothesized that there is a large gap between the number of known annotated enzymes and the actual number in the protein universe, which significantly limits our ability to extract additional biologically relevant functional information from the available sequencing data. To reliably expand the enzyme space, we developed DomSign, a highly accurate domain signature-based enzyme functional prediction tool to assign Enzyme Commission (EC) digits.
  
  
  RESULTS
  DomSign is a top-down prediction engine that yields results comparable, or superior, to those from many benchmark EC number prediction tools, including BLASTP, when a homolog with an identity >30% is not available in the database. Performance tests showed that DomSign is a highly reliable enzyme EC number annotation tool. After multiple tests, the accuracy is thought to be greater than 90%. Thus, DomSign can be applied to large-scale datasets, with the goal of expanding the enzyme space with high fidelity. Using DomSign, we successfully increased the percentage of EC-tagged enzymes from 12% to 30% in UniProt-TrEMBL. In the Kyoto Encyclopedia of Genes and Genomes bacterial database, the percentage of EC-tagged enzymes for each bacterial genome could be increased from 26.0% to 33.2% on average. Metagenomic mining was also efficient, as exemplified by the application of DomSign to the Human Microbiome Project dataset, recovering nearly one million new EC-labeled enzymes.
  
  
  CONCLUSIONS
  Our results offer preliminarily confirmation of the existence of the hypothesized huge number of "hidden enzymes" in the protein universe, the identification of which could substantially further our understanding of the metabolisms of diverse organisms and also facilitate bioengineering by providing a richer enzyme resource. Furthermore, our results highlight the necessity of using more advanced computational tools than BLAST in protein database annotations to extract additional biologically relevant functional information from the available biological sequences.
authors.affiliation: Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. wtm12@mails.tsinghua.edu.cn.|Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China. wtm12@mails.tsinghua.edu.cn.
authors.forename: Tianmin
authors.initials: T
authors.lastname: Wang
authors.affiliation: Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. mori.h.af@m.titech.ac.jp.|Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-E3-10 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. mori.h.af@m.titech.ac.jp.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Mori
authors.affiliation: Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China. chongzhang@mail.tsinghua.edu.cn.
authors.forename: Chong
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. ken@bio.titech.ac.jp.|Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-E3-10 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. ken@bio.titech.ac.jp.
authors.forename: Ken
authors.initials: K
authors.lastname: Kurokawa
authors.affiliation: Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China. xhxing@mail.tsinghua.edu.cn.
authors.forename: Xin-Hui
authors.initials: XH
authors.lastname: Xing
authors.affiliation: Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. takuji@bio.titech.ac.jp.
authors.forename: Takuji
authors.initials: T
authors.lastname: Yamada
mesh_terms: D030562:Databases, Protein; D004798:Enzymes / Q000737:chemistry*; D016680:Genome, Bacterial; D006801:Humans; D056186:Metagenomics; D058977:Molecular Sequence Annotation / Q000379:methods*; D017434:Protein Structure, Tertiary; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D004798:Enzymes