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How does Reductive Dehalogenase Database (RDaseDB) assign sequences to groups?

A reductive dehalogenase amino acid sequence is considered to be part of an ortholog group (OG) if it shares more than 90% pairwise identity with all current members of an OG. New sequences which cannot be sorted into a group are added as singletons. A more detailed breakdown is described below:

We first ascertain the full-length pairwise amino acid identity of your novel sequence(s) with the best-match protein from the reductive dehalogenase database. This is done using BLASTP searches of your sequence queried against the current reductive dehalogenase amino acid sequence database.

a) If your sequence has less than 90% identity at the amino acid level to any sequence in the current database, it is given a singleton identifier number.

b) If your sequence has greater than or equal to 90% pairwise identity at the amino acid level to a sequence in current database, we identify the group that your sequence belongs to.

This is done in the follows:
i. If the sequence shows higher or equal to 90% identity to all members of an ortholog group, the sequence is added to that group.
ii. If your sequence does not shows higher or equal to 90% identity to all members of an ortholog groups, your sequence cannot be added to the group, but can be described as a close relative to that cluster. The sequence will be given a singleton identifier number and curated by the Edwards lab.
iii. If your sequence shows higher or equal to 90% identity to a sington sequence, a new ortholog group may be constructed once the sequence has curated by the Edwards lab.

Default Blast Parameters for Submission

Cost to open a gap:	11
Cost to extend a gap:	1
Penalty for mismatch:	-3
Reward for match:	2
Expected Value (E-Value):	0.000001

How phylogenetic tree (including user sequence) is constructed?

You can construct a phylogenetic tree including your sequence from the blast result page. This tree (Neighbor Joining) is calculated from an alignment constructed from your sequence and the full database or a selection of sequences. Both the alignment and the tree is constructed by MUSCLE.

Notably, the alignment is not edited, and the resulting tree should only be use as a first approximation of the phylogenetic position of your sequence.

To construct phylogenetic trees for publications we recommend you download the sequences you want to include in the tree, align them in MUSCLE or MAFFT, inspect and edit the alignment manually, and then construct the phylogenetic tree using your favourite software (e.g. IQTree, FastTree, RAxML).

Submission rules

How to submit a sequence to the Reductive Dehalogenase Database (RDaseDB)?

For automatic submissions, we only accept publicly available sequences that have an accession number from Genbank or IMG, and that have been annotated as a reductive dehalogenase. You can submit upto 20 sequences per file.

The sequences must be in fasta format with the following header:

Only sequences with the correct format will be accepted. If you want to discuss submitting sequences without a valid accession number or that have not been annotated as a reductive dehalogenase, please contact us.

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Submission rules

Documentation