blaGES genes discrepancies

TomJove commented 4 months ago

Dear ARPCARD amr_curation team,

I went through the diversity of blaGES genes and corresponding b-lactamases GES proteins and noticed some discrepancies I'd like to point out:

The ARPCARD reference blaGES-7 gene does not encode the same protein as the NCBI NDARO blaGES-7 gene. BLDB uses the same blaGES-7 as ARPCARD.
blaGES-47 to blaGES-59 genes (listed in NDARO) are absent in ARPCARD
Found three more blaGES not numbered yet alleles.

==> My blaGES alleles description, sequences and more information about these discrepancies are freely available for download here: https://tinyurl.com/blaGES-4032024

I am currently going on with more genes and progress are available here: https://sites.google.com/view/thomasjove/analysis

Best, Thomas

bpalcock commented 2 months ago

Hi Thomas, the peptide accession for GES07 in CARD (AAP22974.1) is listed as an identical protein for the NDARO GES-7 accession (AAF28763.2), as is the BLDB accession (ADU79013).

For alleles GES-47 to GES-59, we tend to update beta-lactamases periodically in bulk so I will add these in for the next such update.

Thanks, Brian

TomJove commented 2 months ago

Thank you for replying! My apologies for GES-7, seems I have been confused but indeed both sequences are the same.

arpcard / amr_curation

blaGES genes discrepancies #93