Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0008649 rRNA methyltransferase activity	IEA GO_REF:0000120	MODIFY	Summary: The existing MF term is directionally correct but less informative than the family-specific AMR activity rRNA (guanine-N7-)-methyltransferase activity. Reason: Replace the less-specific existing term 'rRNA methyltransferase activity' with rRNA (guanine-N7-)-methyltransferase activity based on UniProt/CARD determinant identity and the curated ARO->GO mapping. Proposed replacements: rRNA (guanine-N7-)-methyltransferase activity Supporting Evidence: file:genes/KLEPN/rmtD/rmtD-uniprot.txt CC -!- FUNCTION: Specifically methylates the N7 position of guanine 1405 in CC 16S rRNA. Confers resistance to various aminoglycosides. CC {ECO:0000256\|PIRNR:PIRNR015852}.
GO:0046677 response to antibiotic	IEA GO_REF:0000120	ACCEPT	Summary: The gene product is an antimicrobial-resistance determinant, so the antibiotic-response annotation is retained. Reason: The CARD/ARO determinant identity supports an antibiotic-resistance biological role. Supporting Evidence: file:genes/KLEPN/rmtD/rmtD-uniprot.txt CC -!- FUNCTION: Specifically methylates the N7 position of guanine 1405 in CC 16S rRNA. Confers resistance to various aminoglycosides. CC {ECO:0000256\|PIRNR:PIRNR015852}.
GO:0046677 response to antibiotic	TAS Reactome:R-HSA-9913143	ACCEPT	Summary: The gene product is an antimicrobial-resistance determinant, so the antibiotic-response annotation is retained. Reason: The CARD/ARO determinant identity supports an antibiotic-resistance biological role. Supporting Evidence: file:genes/KLEPN/rmtD/rmtD-uniprot.txt CC -!- FUNCTION: Specifically methylates the N7 position of guanine 1405 in CC 16S rRNA. Confers resistance to various aminoglycosides. CC {ECO:0000256\|PIRNR:PIRNR015852}.
GO:0005829 cytosol	TAS Reactome:R-HSA-9911509	ACCEPT	Summary: The cellular location is compatible with the encoded AMR enzyme and is retained. Reason: The location is consistent with the protein type and existing UniProt/GOA evidence.
GO:0008649 rRNA methyltransferase activity	TAS Reactome:R-HSA-9911509	MODIFY	Summary: The existing MF term is directionally correct but less informative than the family-specific AMR activity rRNA (guanine-N7-)-methyltransferase activity. Reason: Replace the less-specific TAS-supported term 'rRNA methyltransferase activity' with rRNA (guanine-N7-)-methyltransferase activity based on UniProt/CARD determinant identity and the curated ARO->GO mapping. Proposed replacements: rRNA (guanine-N7-)-methyltransferase activity Supporting Evidence: file:genes/KLEPN/rmtD/rmtD-uniprot.txt CC -!- FUNCTION: Specifically methylates the N7 position of guanine 1405 in CC 16S rRNA. Confers resistance to various aminoglycosides. CC {ECO:0000256\|PIRNR:PIRNR015852}.
GO:0070043 rRNA (guanine-N7-)-methyltransferase activity	RCA file:projects/ANTIMICROBIAL_RESISTANCE/aro2go.sssom.yaml	NEW	Summary: NEW candidate annotation from the curated ARO->GO mapping: rRNA (guanine-N7-)-methyltransferase activity. Reason: The UniProt record cross-references a CARD/ARO AMR determinant, and the curated ARO->GO mapping projects the family-specific molecular function rRNA (guanine-N7-)-methyltransferase activity. This focused draft accepts the candidate as a curator lead for this AMR determinant. Supporting Evidence: file:projects/ANTIMICROBIAL_RESISTANCE/data/candidate_new_annotations.tsv B0F9V0 ARO:3002667 ARO:3004271 narrower skos:relatedMatch GO:0070043 rRNA (guanine-N7-)-methyltransferase activity file:genes/KLEPN/rmtD/rmtD-uniprot.txt CC -!- FUNCTION: Specifically methylates the N7 position of guanine 1405 in CC 16S rRNA. Confers resistance to various aminoglycosides. CC {ECO:0000256\|PIRNR:PIRNR015852}.

Core Functions

rmtD methylates 16S rRNA at guanine N7 in the ribosome, protecting the aminoglycoside binding site and contributing to antibiotic resistance.

Molecular Function:

rRNA (guanine-N7-)-methyltransferase activity

Directly Involved In:

response to antibiotic

Cellular Locations:

cytosol

Supporting Evidence:

file:genes/KLEPN/rmtD/rmtD-uniprot.txt
CC -!- FUNCTION: Specifically methylates the N7 position of guanine 1405 in CC 16S rRNA. Confers resistance to various aminoglycosides. CC {ECO:0000256|PIRNR:PIRNR015852}.

References

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

Reactome:R-HSA-9911509

RMTases methylate 16S ribosomal RNA

Reactome:R-HSA-9913143

Antimicrobial resistance

file:genes/KLEPN/rmtD/rmtD-uniprot.txt

UniProt flat file for rmtD (B0F9V0)

UniProt/CARD identity and protein naming for rmtD.

"CC -!- FUNCTION: Specifically methylates the N7 position of guanine 1405 in CC 16S rRNA. Confers resistance to various aminoglycosides. CC {ECO:0000256|PIRNR:PIRNR015852}."

file:projects/ANTIMICROBIAL_RESISTANCE/aro2go.sssom.yaml

Curated ARO to GO mapping set for AMR gene families

Manual ARO-to-GO mappings used to identify focused AMR annotation gains.

"mapping_set_title: ARO to GO mapping (AMR gene families and resistance mechanisms)"

file:projects/ANTIMICROBIAL_RESISTANCE/data/candidate_new_annotations.tsv

Annotation-gain candidates from ARO to GO mappings

Candidate GO annotations projected from the ARO-to-GO mapping set.

"Candidate GO annotations that UniProtKB entries with a CARD cross-reference would gain from the"

Suggested Experiments

Experiment: Biochemically assay purified rmtD against representative antibiotic substrates for the inferred AMR family and measure loss of drug activity or target modification.

Type: in vitro enzyme assay

📚 Additional Documentation

Notes

(rmtD-notes.md)

Notes: rmtD

Focused AMR batch review. UniProt accession: B0F9V0. Source organism: Klebsiella pneumoniae.

UniProt/CARD provenance: DR CARD; ARO:3002667; rmtD; ARO:0001001; antibiotic target alteration.
ARO-to-GO candidate: GO:0070043 (rRNA (guanine-N7-)-methyltransferase activity) from projects/ANTIMICROBIAL_RESISTANCE/data/candidate_new_annotations.tsv and projects/ANTIMICROBIAL_RESISTANCE/aro2go.sssom.yaml.
This is a DRAFT focused review intended to cover the AMR annotation gap; it has not had a gene-specific deep-research pass.

📄 View Raw YAML

id: B0F9V0
gene_symbol: rmtD
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:573
  label: Klebsiella pneumoniae
description: rmtD encodes a 16S rRNA G1405 N7 methyltransferase in Klebsiella pneumoniae. UniProt/CARD identify this entry as an acquired aminoglycoside-resistance methyltransferase; methylation of 16S rRNA protects the ribosomal A site from clinically important aminoglycosides. UniProt names the protein '16S rRNA (guanine(1405)-N(7))-methyltransferase' (accession B0F9V0).
existing_annotations:
- term:
    id: GO:0008649
    label: rRNA methyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: The existing MF term is directionally correct but less informative than the family-specific AMR activity rRNA (guanine-N7-)-methyltransferase activity.
    action: MODIFY
    reason: Replace the less-specific existing term 'rRNA methyltransferase activity' with rRNA (guanine-N7-)-methyltransferase activity based on UniProt/CARD determinant identity and the curated ARO->GO mapping.
    proposed_replacement_terms:
    - id: GO:0070043
      label: rRNA (guanine-N7-)-methyltransferase activity
    supported_by:
    - reference_id: file:genes/KLEPN/rmtD/rmtD-uniprot.txt
      supporting_text: 'CC   -!- FUNCTION: Specifically methylates the N7 position of guanine 1405 in

        CC       16S rRNA. Confers resistance to various aminoglycosides.

        CC       {ECO:0000256|PIRNR:PIRNR015852}.'
- term:
    id: GO:0046677
    label: response to antibiotic
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: involved_in
  review:
    summary: The gene product is an antimicrobial-resistance determinant, so the antibiotic-response annotation is retained.
    action: ACCEPT
    reason: The CARD/ARO determinant identity supports an antibiotic-resistance biological role.
    supported_by:
    - reference_id: file:genes/KLEPN/rmtD/rmtD-uniprot.txt
      supporting_text: 'CC   -!- FUNCTION: Specifically methylates the N7 position of guanine 1405 in

        CC       16S rRNA. Confers resistance to various aminoglycosides.

        CC       {ECO:0000256|PIRNR:PIRNR015852}.'
- term:
    id: GO:0046677
    label: response to antibiotic
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9913143
  qualifier: involved_in
  review:
    summary: The gene product is an antimicrobial-resistance determinant, so the antibiotic-response annotation is retained.
    action: ACCEPT
    reason: The CARD/ARO determinant identity supports an antibiotic-resistance biological role.
    supported_by:
    - reference_id: file:genes/KLEPN/rmtD/rmtD-uniprot.txt
      supporting_text: 'CC   -!- FUNCTION: Specifically methylates the N7 position of guanine 1405 in

        CC       16S rRNA. Confers resistance to various aminoglycosides.

        CC       {ECO:0000256|PIRNR:PIRNR015852}.'
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9911509
  qualifier: located_in
  review:
    summary: The cellular location is compatible with the encoded AMR enzyme and is retained.
    action: ACCEPT
    reason: The location is consistent with the protein type and existing UniProt/GOA evidence.
- term:
    id: GO:0008649
    label: rRNA methyltransferase activity
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9911509
  qualifier: enables
  review:
    summary: The existing MF term is directionally correct but less informative than the family-specific AMR activity rRNA (guanine-N7-)-methyltransferase activity.
    action: MODIFY
    reason: Replace the less-specific TAS-supported term 'rRNA methyltransferase activity' with rRNA (guanine-N7-)-methyltransferase activity based on UniProt/CARD determinant identity and the curated ARO->GO mapping.
    proposed_replacement_terms:
    - id: GO:0070043
      label: rRNA (guanine-N7-)-methyltransferase activity
    supported_by:
    - reference_id: file:genes/KLEPN/rmtD/rmtD-uniprot.txt
      supporting_text: 'CC   -!- FUNCTION: Specifically methylates the N7 position of guanine 1405 in

        CC       16S rRNA. Confers resistance to various aminoglycosides.

        CC       {ECO:0000256|PIRNR:PIRNR015852}.'
- term:
    id: GO:0070043
    label: rRNA (guanine-N7-)-methyltransferase activity
  evidence_type: RCA
  original_reference_id: file:projects/ANTIMICROBIAL_RESISTANCE/aro2go.sssom.yaml
  qualifier: enables
  review:
    summary: 'NEW candidate annotation from the curated ARO->GO mapping: rRNA (guanine-N7-)-methyltransferase activity.'
    action: NEW
    reason: The UniProt record cross-references a CARD/ARO AMR determinant, and the curated ARO->GO mapping projects the family-specific molecular function rRNA (guanine-N7-)-methyltransferase activity. This focused draft accepts the candidate as a curator lead for this AMR determinant.
    additional_reference_ids:
    - file:projects/ANTIMICROBIAL_RESISTANCE/data/candidate_new_annotations.tsv
    - file:genes/KLEPN/rmtD/rmtD-uniprot.txt
    supported_by:
    - reference_id: file:projects/ANTIMICROBIAL_RESISTANCE/data/candidate_new_annotations.tsv
      supporting_text: "B0F9V0\tARO:3002667\tARO:3004271\tnarrower\tskos:relatedMatch\tGO:0070043\trRNA (guanine-N7-)-methyltransferase activity"
    - reference_id: file:genes/KLEPN/rmtD/rmtD-uniprot.txt
      supporting_text: 'CC   -!- FUNCTION: Specifically methylates the N7 position of guanine 1405 in

        CC       16S rRNA. Confers resistance to various aminoglycosides.

        CC       {ECO:0000256|PIRNR:PIRNR015852}.'
references:
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: Reactome:R-HSA-9911509
  title: RMTases methylate 16S ribosomal RNA
  findings: []
- id: Reactome:R-HSA-9913143
  title: Antimicrobial resistance
  findings: []
- id: file:genes/KLEPN/rmtD/rmtD-uniprot.txt
  title: UniProt flat file for rmtD (B0F9V0)
  findings:
  - statement: UniProt/CARD identity and protein naming for rmtD.
    supporting_text: 'CC   -!- FUNCTION: Specifically methylates the N7 position of guanine 1405 in

      CC       16S rRNA. Confers resistance to various aminoglycosides.

      CC       {ECO:0000256|PIRNR:PIRNR015852}.'
- 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: rmtD methylates 16S rRNA at guanine N7 in the ribosome, protecting the aminoglycoside binding site and contributing to antibiotic resistance.
  molecular_function:
    id: GO:0070043
    label: rRNA (guanine-N7-)-methyltransferase activity
  directly_involved_in:
  - id: GO:0046677
    label: response to antibiotic
  supported_by:
  - reference_id: file:genes/KLEPN/rmtD/rmtD-uniprot.txt
    supporting_text: 'CC   -!- FUNCTION: Specifically methylates the N7 position of guanine 1405 in

      CC       16S rRNA. Confers resistance to various aminoglycosides.

      CC       {ECO:0000256|PIRNR:PIRNR015852}.'
  locations:
  - id: GO:0005829
    label: cytosol
suggested_questions:
- question: Is the ARO-derived rRNA (guanine-N7-)-methyltransferase activity annotation sufficiently specific for rmtD, or is a narrower substrate/site-specific GO term warranted?
  experts: []
suggested_experiments:
- description: Biochemically assay purified rmtD against representative antibiotic substrates for the inferred AMR family and measure loss of drug activity or target modification.
  experiment_type: in vitro enzyme assay

rmtD

Gene Description