Sep 28, 2016

HydDB: A web tool for hydrogenase classification and analysis

Scientific Reports
Dan SøndergaardChris Greening

Abstract

H2 metabolism is proposed to be the most ancient and diverse mechanism of energy-conservation. The metalloenzymes mediating this metabolism, hydrogenases, are encoded by over 60 microbial phyla and are present in all major ecosystems. We developed a classification system and web tool, HydDB, for the structural and functional analysis of these enzymes. We show that hydrogenase function can be predicted by primary sequence alone using an expanded classification scheme (comprising 29 [NiFe], 8 [FeFe], and 1 [Fe] hydrogenase classes) that defines 11 new classes with distinct biological functions. Using this scheme, we built a web tool that rapidly and reliably classifies hydrogenase primary sequences using a combination of k-nearest neighbors' algorithms and CDD referencing. Demonstrating its capacity, the tool reliably predicted hydrogenase content and function in 12 newly-sequenced bacteria, archaea, and eukaryotes. HydDB provides the capacity to browse the amino acid sequences of 3248 annotated hydrogenase catalytic subunits and also contains a detailed repository of physiological, biochemical, and structural information about the 38 hydrogenase classes defined here. The database and classifier are freely and publicly available ...Continue Reading

  • References42
  • Citations79

References

Mentioned in this Paper

Metabolic Process, Cellular
Classification
Enzymes, antithrombotic
Hydrogenase
Archaea
Craniodiaphyseal Dysplasia, Autosomal Dominant (Disorder)
Metabolic Pathway
Enzymes for Treatment of Wounds and Ulcers
Phyla
Cyclic AMP-Dependent Protein Kinase Catalytic Subunits

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