HydDB database

Introduction

The hydrogenase database (HydDB) provides information pages for different groups of hydrogenases (Søndergaard, Pedersen, and Greening 2016). These could originally queried using the HydDB webserver but is no longer maintained, however, the database itself is available here and there is active work on HydDB v2.0.

For a brief description about the different hydrogenases, have a look at Table 1 in this paper.

Installation

Available on crunchomics: Yes,

• The HydDB database is installed as part of the bioinformatics share. If you have access to Crunchomics and have not yet access to the bioinformatics you can send an email with your Uva netID to Nina Dombrowski.

The database can be found here:

• /zfs/omics/projects/bioinformatics/databases/hydDB/release2022.

If you want to download the database yourself, you can do:

# Download the data
wget https://raw.githubusercontent.com/GreeningLab/HydDB/refs/heads/main/fastas/HydDB_all_hydrogenases.faa 

# Convert faa file to diamond database
diamond makedb --in HydDB_all_hydrogenases.faa -d hyddb

Example usage

The database can be searched with diamond blastp and we provide a small python script to parse the output:

## Run search
diamond blastp -q data/genomes.faa \
    --more-sensitive --evalue 1e-3 \
    --threads 5 --max-target-seqs 20 \
    --db /zfs/omics/projects/bioinformatics/databases/hyddb/release2022/hyddb \
    --outfmt 6 qseqid qtitle qlen sseqid salltitles slen qstart qend sstart send evalue bitscore length pident \
    --out results/results.txt

# Parse the data
python /zfs/omics/projects/bioinformatics/databases/hyddb/release2022/parse_diamond_hydDB.py \
    -i results/results.txt \
    -o results/hyddb_parsed.tsv \
    --evalue 1e-5

The python returns the best hit based on the e-value and bitscore. It also discards hits below a certain e-value thresholds and below the following percent identities (as recommended here):

• [NiFe] = >50% for group 4, >30% for all other groups
• [FeFe] = >45%
• [Fe] = >50%

options:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input HMMER tblout file
  -o OUTPUT, --output OUTPUT
                        Output filtered TSV file
  --evalue EVALUE       E-value cutoff (default: 1e-10)
  --cutoff-fefe CUTOFF_FEFE
                        Percent identity cutoff for FeFe hydrogenases (default: 45)
  --cutoff-nife-all CUTOFF_NIFE_ALL
                        Percent identity cutoff for NiFe Groups 1, 2, 3 (default: 30)
  --cutoff-nife-group-4 CUTOFF_NIFE_GROUP_4
                        Percent identity cutoff for NiFe Group 4 (default: 50)
  --cutoff-feonly CUTOFF_FEONLY
                        Percent identity cutoff for Fe-only hydrogenases (default: 50)

References

Søndergaard, Dan, Christian N. S. Pedersen, and Chris Greening. 2016. “HydDB: A Web Tool for Hydrogenase Classification and Analysis.” Scientific Reports 6 (1). https://doi.org/10.1038/srep34212.