OXA-116 in CARD and NCBI

[agmcarthur]

OXA-116 is a partial gene in CARD but listed at NCBI's Reference Gene Catalog. @danielhhaft do you have additional data on this gene or perhaps partials are not supported in the NCBI Reference Gene Catalog? Thanks!

[iorga]

Hi @agmcarthur ,

OXA-116 has been superseded by OXA-698, which contains the full sequence.

All the best, Bogdan

[bpalcock]

hi Bogdan, do you know somewhere we could access a list of all the OXA numberings that have been superseded by another allele (or indeed for all Beta-lactamases)?

thanks, brian

[iorga]

Hi Brian,

To my knowledge there is not such a list. Over the time I tried to gather all the information available from different places and include it in the BLDB.

• On the original Lahey site there are a few mentions of beta-lactamases that have identical sequences, and these became alternative names.
• There were also a few cases of duplicate or partial sequences in the beta-lactamase families maintained by the Pasteur Institute (LEN, OKP, OXY), that were cleaned up a few years ago.
• In the PDC family, there was a paper reporting several new beta-lactamases for which only partial sequences (with the signal peptide missing) were deposited. During the following years, when the complete sequences became available, they replaced the partial ones with the same allele number (when the authors or the curators were aware of the existence of the partial sequences) or with a different allele number (which would supersede the old one afterwards).
• More generally, this happens for historical reasons, there are still some allele numbers assigned in the original Lahey repository to partial sequences, for which no complete sequences are available to date. Typical examples are CMY-98 (partial sequence), OXA-16 (partial sequence), OXA-186 to OXA-191 (for which the sequences were reported in the paper, but never deposited), OXA-410 (partial sequence, but while writing this message I checked and a complete sequence is available now - I will open a separate issue for this).

Over the time these problems will be fixed, with the help of the community, but it is important to keep trace of these changes.

Bogdan

[bpalcock]

Thanks Bogdan - I might make it one of my summer projects to better harmonize BLDB and CARD to catch these issues