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A public repository for collective curation of antimicrobial resistance (AMR) genes and mutations. Submit, discuss, and resolve AMR curation issues.
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Question on sequence update of mecC-type BlaZ gene in CARD v 3.1 to 3.2 #79

Closed katrinakalantar closed 3 months ago

katrinakalantar commented 1 year ago

Hello! I have a question about a sequence update (details below) and was curious to learn more about how the decision was made to update this sequence / the evidence for or against the initial sequence. We were seeing some interesting hits to the old sequence, but it seems to no longer be in the databases. Any additional information would be much appreciated.

The changelog from CARD DB v3.1.4 to v3.2.0 indicates that the sequence of mecC-type BlaZ was updated from FR823292 to FR823292.1, which has an entirely different (apparently non-overlapping) sequence.

3829 UPDATE mecC-type BlaZ penam; antibiotic inactivation; BlaZ beta-lactamase; penicillin; ARO_description; model_sequences; ARO_category "UPDATED ARO_description with A blaZ-like beta-lactamase found in S. Aureus. UPDATED partial with 0 UPDATED sequence with TTGAAAAAATTAATAATTTTAGTCGTGTTAGCGTTGATATTAAGTGCTTGTAATAGTAAGAATTCAACTAATAACGACATTGAAAAGATCGAAAAAAAATATGGTGCTAACGTAGGTATGTATGCTCTTAATACTCAAAATGGTAAAGAATTATCATTTAATGAAAATAAGCGTTTTGCATATGCTTCCACATTAAAAACTATAAGTAGCGCAATGCTGCTTGAACAAACACCTTACAACAAATTAGATAAAAAAATTCACATTAATAAAGATGATATTGTTCCATATTCACCAGTGTTAGAAAAATATATTGGCAAAGAGATAACTTTAAAAAAGCTTATAGAAGCTACCATGTTATTTAGCGATAACACGGCTAATAATAAAATTATCGATGAATTGGGAGGATATGGGCAAGTAAAAACGAAACTGATAGATTTAGGCGATACAACGACACATCCATCTAGAAAAGAACCAGACTTAAATTTTTATTCACCAAAGGATAAACGAGATACAAGTACTCCATTAGCCTATGGTAAAACTTTAAAGAAACTTATAGCTGATGGAGATCTTAGCAAAGCAAACAAAGATTTCTTACTTAATCTAATGTTCAAAAATAAAAGTGGCGATACATTAATTAAGGATGGTGCACCTTCAAACTTTAAAGTTATGGATAAGAGCGGTCAAGCACTAACATACGGTTCAAGAAACGATGTTGCGTTTGTTTATCCAGATGGACAAGATAAACCTATAATTCTGGTGATATTTACAAATAAAGATAGAAAAGATGGTAAACCTAATGACAAAATAGTAAGTGAGGTTGCTGAAATTGTACTAAAAAATATTAATGAGTAA UPDATED fmax with 1647 UPDATED accession with FR823292.1

[for reference, the sequence was in CARD DB v. 3.1.4]

gb|FR823292|+|0-480|ARO:3005097|mecC-type BlaZ [Staphylococcus aureus] Partial ATGAAAATCACCATTTTAGCTGTAGGGAAACTAAAAGAGAAATATTGGAAGCAAGCCATAGCAGAATATGAAAAACGTTTAGGCCCATACACCAAGATAGACATCATAGAAGTTCCAGACGAAAAAGCACCAGAAAATATGAGCGACAAAGAAATCGAGCAAGTAAAAGAAAAAGAAGGGCAACGAATACTAGCCAAAATCAAACCACAATCAACAGTCATTACATTAGAAATACAAGGAAAGATGCTATCTTCCGAAGGATTGGCCCAAGAATTGAACCAACGCATGACCCAAGGGCAAAGCGACTTTGTATTCGTCATTGGCGGATCAAATGGCCTGCACAAGGACGTCTTACAACGCAGTAACTACGCACTATCATTCAGCAAAATGACATTTCCACATCAAATGATGCGGGTTGTGTTAATTGAGCAAGTGTATAGAGCGTTTAAGATTATGCGCGGAGAAGCGTATCACAAATGA

danielhhaft commented 1 year ago

(NCBI member Daniel Haft here, taking a quick look) The old sequence translates to WP_000704775.1, 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH. That should be just a housekeeping gene, not an antimicrobial resistance gene, so it looks like CARD had that particular sequence by mistake.

The new sequence translates to CBZ41939.1, protein product of the blaZ gene of the mecZ locus. CBZ41939.1 is the correct protein.

Since CARD's change appears to have been simply a case of replacing the wrong sequence with the right one, I imagine this ticket could be resolved now.

bpalcock commented 3 months ago

Very delayed response but Dan is correct - this does happen occasionally when an incorrect sequence is grabbed by mistake