cfr

Summary: Technically true but too broad to be useful for Cfr.

Reason: Following the RADICAL_SAM project rule for the generic domain-derived rows (projects/RADICAL_SAM.md): the row is true, so it is refined rather than flagged as an over-annotation. Cfr has a defined reaction, methylation of C8 of adenine 2503 in 23S rRNA, and GO:0016433 is the term this entry already carries for it.

Proposed replacements: rRNA (adenine) methyltransferase activity

Summary: Correct location for a bacterial rRNA-modifying enzyme.

Reason: The UniProt record carries cytoplasm as the subcellular-location-derived GO annotation.

Summary: Broad process annotation that should be replaced by rRNA base methylation for Cfr.

Reason: Cfr performs a base methylation on mature 23S rRNA. GO:0070475 is the better process-level representation than generic rRNA processing.

Proposed replacements: rRNA base methylation

Summary: Incorrect electronic carryover from broad methylthiotransferase signatures.

Reason: The Cfr record and Cfr mechanism literature identify 23S rRNA A2503 as the substrate. This review found no support that Cfr modifies tRNA.

Summary: Correct but broad; replace with rRNA (adenine) methyltransferase activity.

Reason: Cfr is an rRNA adenine methyltransferase, not a generic RNA methyltransferase. GO still lacks the exact C8/A2503 child term.

Proposed replacements: rRNA (adenine) methyltransferase activity

Summary: Correct core molecular-function parent for Cfr, but missing the C8/A2503 specificity.

Reason: Cfr methylates adenine in 23S rRNA. The existing term is the best current GO parent; a Cfr-specific A2503 C8 term is proposed below.

Summary: Correct but too broad; replace with rRNA (adenine) methyltransferase activity.

Reason: Generic transferase activity is a weak representation of Cfr compared with GO:0016433.

Proposed replacements: rRNA (adenine) methyltransferase activity

Summary: Plausible substrate-binding annotation, but secondary to catalytic methyltransferase activity.

Reason: Cfr acts on 23S rRNA, but substrate binding is not the core evolved function.

Summary: Incorrect TreeGrafter propagation for Cfr.

Reason: Retained. Cfr's characterized substrate is 23S rRNA: it methylates C8 of adenosine 2503 (PMID:19144912), and the record's rRNA methyltransferase, rRNA base methylation and rRNA binding rows are accepted. The tRNA specificity in this family belongs to the paralogous radical-SAM enzyme RlmN, which methylates C2 of A2503 in 23S rRNA and of A37 in tRNA; Cfr lacks the tRNA activity, so this row is a substrate-class error propagated from the shared RlmN/Cfr PANTHER family rather than a merely coarse term. No tRNA substrate is reported for Cfr in the UniProt record or the cited literature.

Summary: Broad cofactor-binding term; the 4Fe-4S child is more informative and already annotated.

Reason: Replace broad iron-sulfur cluster binding with the specific 4Fe-4S cluster binding annotation for Cfr.

Proposed replacements: 4 iron, 4 sulfur cluster binding

Summary: Correct cofactor-binding annotation for a radical SAM Cfr enzyme.

Reason: Core cofactor binding under the project rule. The [4Fe-4S] cluster is not merely required for the mechanism: it generates the 5'-deoxyadenosyl radical that abstracts the C8 hydrogen, which is the step that distinguishes Cfr from the conventional SAM methyltransferases. Catalysis is established, so ACCEPT rather than KEEP_AS_NON_CORE.

Summary: Correct process annotation for the Cfr-catalyzed rRNA A2503 methylation.

Reason: Cfr directly methylates a base in 23S rRNA; the process term is appropriate.

Summary: NEW high-level process annotation for Cfr-mediated multidrug resistance.

Reason: Cfr-mediated A2503 C8 methylation provides resistance to multiple peptidyl-transferase-center antibiotic classes. This is a high-level process annotation, while the core curation need remains the C8-specific molecular-function term.

Summary: cfr binds S-adenosyl-L-methionine at the unique iron of its radical SAM [4Fe-4S] cluster and cleaves it to the 5'-deoxyadenosyl radical; two SAM are consumed per methyl transferred, one as the methyl donor and one as the radical source.

Reason: Not in GOA. Added under the RADICAL_SAM treatment rule, which treats GO:1904047 as a core cosubstrate-binding function of every radical SAM enzyme whose catalysis is established. This is a molecular function the protein itself performs, so the participation test is met directly: cfr binds SAM and cleaves it, rather than merely being required for a process that consumes it. UniProt's curated cofactor note records the exchangeable S-adenosyl-L-methionine on the radical SAM cluster and the entry's binding features name the 4Fe-4S-S-AdoMet ligand, so the claim rests on curated record content rather than on an electronic GO line. Coded IC because the inference is the reviewer's, drawn from that curated content and the established rRNA (adenine) methyltransferase activity rather than from a SAM-binding assay on this protein. Comparator check, against GOA rather than against this project's own proposals: GOA does annotate GO:1904047 to radical SAM enzymes in exactly this role, by UniRule -- ECOLI/queE (UR000100349), ECOLI/moaA and PSEPK/moaA (UR000101305), METEA/pqqE and PSEPK/pqqE (UR000098303). So the absence here is patchy UniRule coverage, which rules happen to carry the term, not a GO convention against annotating a radical SAM enzyme's own cosubstrate. That is also why those five genes have an existing row to ACCEPT or MODIFY while this one needs a NEW row.