HydDB provides access to an accurate classifier for hydrogenase sequences and a curated database of hydrogenases by known type. The service is provided by the School of Biological Sciences, Monash University and the Bioinformatics Research Centre, Aarhus University.


Dear HydDB user,

A user recently discovered a bug in the HydDB classifier which caused a high number of sequences to be falsely classified as non-hydrogenases. This may have caused wrong and confusing results for a wide range of users. We sincerely apologize for any inconvenience caused by the bug, which has now been fixed. Users should now experience a much more accurate prediction of hydrogenasity.

We hope that HydDB will remain a valuable tool for our users and greatly appreciate all user feedback.

If enabled, HydDB will use CDD to check whether the submitted sequences encode catalytic subunits of putative before classification. Since this step is time-consuming, you may want to uncheck this option if you are certain your sequences encode hydrogenase catalytic subunits.

If an e-mail address is provided, a mail will be sent when the job succeeds or fails.


To use the classifier to predict the type of one or more hydrogenases from sequence, either:

  • paste your FASTA-formatted protein sequences into the text area, or
  • upload a FASTA-formatted file with your protein sequences.

Press the "Submit" button to upload the sequences and begin the classification.

If you provided an e-mail address you will receive an e-mail when your job finishes or fails including a link to the results. You will also be able to download the results as a CSV file.

Only sequences encoding the catalytic subunits of hydrogenases will be classified, i.e. those binding the [NiFe]-centre (NiFe-hydrogenases), [FeFe]-centre (FeFe-hydrogenases), or [Fe]-centre (Fe-hydrogenases). Electron-transfer subunits, accessory proteins, and maturation factors cannot be classified by this service.


A job can at most run for 2 hours and atmost 4000 sequences can be submitted. This should be enough for about 2500 sequences to be classified. Results will be stored for 2 weeks. However, we recommend to download the results as they may be deleted due to the rare event of a power outage or server crash.


Jobs completed in total 2976
Sequences classified in total 1398659
Jobs completed in the last 24 hours 18
Sequences classified in the last 24 hours 18