Hydrogenase Catalytic Subunit Sequence Database

The database was constructed using the amino acid sequences of all curated non-redundant 3248 hydrogenase catalytic subunits represented in the NCBI RefSeq database in August 20142 (link) (Dataset S1). In order to test the classification tool, additional sequences from newly-sequenced archaeal and bacterial phyla were retrieved from the Joint Genome Institute’s Integrated Microbial Genomes database43 (link).

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Søndergaard D., Pedersen C.N, & Greening C. (2016). HydDB: A web tool for hydrogenase classification and analysis. Scientific Reports, 6, 34212.

Publication 2016

Amino acid sequences Archaeal Bacterial Catalytic subunits Genome Hydrogenase Joint Microbial genomes

Corresponding Organization :

Other organizations : Aarhus University, CSIRO Land and Water, Commonwealth Scientific and Industrial Research Organisation

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Protocol cited in 108 other protocols

Variable analysis

independent variables

Amino acid sequences of all curated non-redundant 3248 hydrogenase catalytic subunits represented in the NCBI RefSeq database in August 2014
Additional sequences from newly-sequenced archaeal and bacterial phyla retrieved from the Joint Genome Institute's Integrated Microbial Genomes database

dependent variables

Not explicitly mentioned

control variables

Not explicitly mentioned

controls

No positive or negative controls were specified by the authors.

Annotations

Based on most similar protocols

Optimize protein sequence alignment by using MUSCLE (v.3.8.31) and trimming with TrimAL (-gt 0.05 -cons 50) to obtain reliable phylogenetic information (Protocol 1).

Use PSI-BLAST with modified settings to return 500 hits and eliminate any query with less than 80% coverage to maximize the identification of NiFe membrane-bound hydrogenase sequences (Protocol 2).

Construct a maximum-likelihood phylogenetic tree with bootstrapping (500 replicates) to investigate the distribution and evolutionary history of group 2a [NiFe]-hydrogenases, and manually analyze representative genomes to identify putative gene clusters (Protocol 3).

Subsampling metatranscriptome data to 10 million reads per sample and using Diamond to compare against the HydDB hydrogenase database with identity >65% and alignment length >40 aa can provide reliable quantification of hydrogenase gene expression (Protocol 4).

Verify the consistency of the neighboring genes of each catalytic subunit with the subunits expected in the hydrogenase class-specific template to trace the possible structural composition of putative hydrogenases (Protocol 5).

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