id: P10337
gene_symbol: ermF
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:817
  label: Bacteroides fragilis
description: ermF encodes an Erm-family 23S rRNA adenine-N6 methyltransferase in Bacteroides fragilis. UniProt/CARD identify this entry as a macrolide-lincosamide-streptogramin resistance determinant; methylation of 23S rRNA alters the macrolide binding site on the large ribosomal subunit. UniProt names the protein 'rRNA adenine N-6-methyltransferase' (accession P10337).
existing_annotations:
- term:
    id: GO:0000154
    label: rRNA modification
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: The rRNA modification/methylation process is consistent with an Erm-family 23S rRNA methyltransferase.
    action: ACCEPT
    reason: Erm enzymes confer resistance by methylating 23S rRNA; this process annotation is biologically appropriate.
    supported_by:
    - reference_id: file:genes/BACFG/ermF/ermF-uniprot.txt
      supporting_text: 'CC   -!- FUNCTION: Involved in erythromycin resistance.'
- term:
    id: GO:0000179
    label: rRNA (adenine-N6,N6-)-dimethyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: The existing dimethyltransferase term is retained as the more specific molecular function for this Erm-family enzyme.
    action: ACCEPT
    reason: GO:0000179 is a child of the broader rRNA adenine-N6 methyltransferase activity and captures the N6,N6-dimethylation activity expected for Erm-mediated macrolide-lincosamide-streptogramin resistance.
    supported_by:
    - reference_id: file:genes/BACFG/ermF/ermF-uniprot.txt
      supporting_text: 'CC   -!- FUNCTION: Involved in erythromycin resistance.'
- term:
    id: GO:0031167
    label: rRNA methylation
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  qualifier: involved_in
  review:
    summary: The rRNA modification/methylation process is consistent with an Erm-family 23S rRNA methyltransferase.
    action: ACCEPT
    reason: Erm enzymes confer resistance by methylating 23S rRNA; this process annotation is biologically appropriate.
    supported_by:
    - reference_id: file:genes/BACFG/ermF/ermF-uniprot.txt
      supporting_text: 'CC   -!- FUNCTION: Involved in erythromycin resistance.'
- term:
    id: GO:0046677
    label: response to antibiotic
  evidence_type: RCA
  original_reference_id: file:projects/ANTIMICROBIAL_RESISTANCE/aro2go.sssom.yaml
  qualifier: involved_in
  review:
    summary: 'NEW process annotation: ermF is an AMR determinant involved in antibiotic response/resistance.'
    action: NEW
    reason: CARD/ARO identity places this gene in an antimicrobial-resistance determinant family; response to antibiotic is the appropriate high-level GO biological process for the resistance role.
    additional_reference_ids:
    - file:genes/BACFG/ermF/ermF-uniprot.txt
    supported_by:
    - reference_id: file:genes/BACFG/ermF/ermF-uniprot.txt
      supporting_text: DR   CARD; ARO:3000498; ErmF; ARO:0001001; antibiotic target alteration.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000118
  title: TreeGrafter-generated GO annotations
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: file:genes/BACFG/ermF/ermF-uniprot.txt
  title: UniProt flat file for ermF (P10337)
  findings:
  - statement: UniProt/CARD identity and protein naming for ermF.
    supporting_text: 'CC   -!- FUNCTION: Involved in erythromycin resistance.'
- id: file:projects/ANTIMICROBIAL_RESISTANCE/aro2go.sssom.yaml
  title: Curated ARO to GO mapping set for AMR gene families
  findings:
  - statement: Manual ARO-to-GO mappings used to identify focused AMR annotation gains.
    supporting_text: 'mapping_set_title: ARO to GO mapping (AMR gene families and resistance mechanisms)'
- id: file:projects/ANTIMICROBIAL_RESISTANCE/data/candidate_new_annotations.tsv
  title: Annotation-gain candidates from ARO to GO mappings
  findings:
  - statement: Candidate GO annotations projected from the ARO-to-GO mapping set.
    supporting_text: Candidate GO annotations that UniProtKB entries with a CARD cross-reference would gain from the
core_functions:
- description: ermF methylates adenine N6 in 23S rRNA, modifying the antibiotic target site in the large ribosomal subunit and contributing to macrolide/lincosamide/streptogramin resistance.
  molecular_function:
    id: GO:0000179
    label: rRNA (adenine-N6,N6-)-dimethyltransferase activity
  directly_involved_in:
  - id: GO:0046677
    label: response to antibiotic
  supported_by:
  - reference_id: file:genes/BACFG/ermF/ermF-uniprot.txt
    supporting_text: 'CC   -!- FUNCTION: Involved in erythromycin resistance.'
suggested_questions:
- question: Is the ARO-derived rRNA (adenine-N6-)-methyltransferase activity annotation sufficiently specific for ermF, or is a narrower substrate/site-specific GO term warranted?
  experts: []
suggested_experiments:
- description: Biochemically assay purified ermF against representative antibiotic substrates for the inferred AMR family and measure loss of drug activity or target modification.
  experiment_type: in vitro enzyme assay