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HydDB: A web tool for hydrogenase classification and analysis

Dan Søndergaard, Christian N. S. Pedersen, Chris Greening
doi: https://doi.org/10.1101/061994
Dan Søndergaard
aAarhus University, Bioinformatics Research Centre, C.F. Møllers Allé 8, Aarhus DK-8000, Denmark
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Christian N. S. Pedersen
aAarhus University, Bioinformatics Research Centre, C.F. Møllers Allé 8, Aarhus DK-8000, Denmark
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Chris Greening
cThe Commonwealth Scientific and Industrial Research Organisation, Land and Water Flagship, Clunies Ross Street, Acton, ACT 2060, Australia
dMonash University, School of Biological Sciences, Clayton, VIC 2800, Australia
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  • For correspondence: chris.greening@monash.edu
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Abstract

H2 metabolism is the most ancient and diverse mechanism of energy-generation. 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]-hydrogenase subgroups, 8 [FeFe]-hydrogenase subtypes, [Fe]-hydrogenases). 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 also provides the capacity to browse 3248 annotated sequences and 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 at http://services.birc.au.dk/hyddb/

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 04, 2016.
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HydDB: A web tool for hydrogenase classification and analysis
Dan Søndergaard, Christian N. S. Pedersen, Chris Greening
bioRxiv 061994; doi: https://doi.org/10.1101/061994
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HydDB: A web tool for hydrogenase classification and analysis
Dan Søndergaard, Christian N. S. Pedersen, Chris Greening
bioRxiv 061994; doi: https://doi.org/10.1101/061994

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