PMID:18443110 A naturally occurring proline-to-alanine amino acid change in Fks1p in Candida parapsilosis, Candida orthopsilosis, and Candida metapsilosis accounts for reduced echinocandin susceptibility.

[CuzickA]

Curated by @jingluodatacurator

https://canto.phi-base.org/curs/6c83025cb4d29f2a

[jingluodatacurator]

Curation completed pending review. Please double check expression level, conditions and comment.

[CuzickA]

We cannot curate the natural sequence variation within FKS1 of Candida parapsilosis, Candida orthopsilosis, and Candida metapsilosis.

We can only curate the section of data using Saccharomyces cerevisiae

[CuzickA]

Current annotation

[CuzickA]

@MPiovesana, when you have a minute please could you have a look at the method in the publication for creating the Sc FKS1 P647A genotype. It is a 2-step method and I think it is essentially a partial gene replacement incorporating the P647A change. In which case the current genotype above with the partial deletion and AA substitution would not be correct. Its a shame that there is no image in the publication to describe it.

[CuzickA]

Hi @jingluodatacurator, similar to the last session I checked in https://github.com/PHI-base/curation/issues/145 the curation needs to be split out into separate annotations rather than being grouped together.

Here are the changes I have made to the above annotation, please let me know if they make sense to you or if they require further explanation

[CuzickA]

Once we have resolved the genotype query I will also change the expression level to not assayed.

[MPiovesana]

@MPiovesana, when you have a minute please could you have a look at the method in the publication for creating the Sc FKS1 P647A genotype. It is a 2-step method and I think it is essentially a partial gene replacement incorporating the P647A change. In which case the current genotype above with the partial deletion and AA substitution would not be correct. Its a shame that there is no image in the publication to describe it.

@CuzickA I have just checked the Materials and Method and the Results sections of the paper, and indeed the 2-step method (deletion followed by homologous recombination) results in a partial gene replacement, where the only difference between the wild type and the mutant alleles is the presence of the P647A mutation. So I believe this genotype can be annotated as an amino acid substitution, and the deletion can be omitted as it was only a step in the gene replacement technique employed by the authors.

[CuzickA]

Thanks @MPiovesana

Genotype now updated to

Annotations now look like this

[CuzickA]

Session now approved. I will leave this ticket open until @jingluodatacurator has had a chance to look at the comments and then I will close it.

[CuzickA]

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