cbcW

Summary: Transport is right but the substrate class is wrong; GO does not place carnitine, glycine betaine or choline transport under amine transport.

Reason: An OLS4 query of the GO hierarchy (cbcW-bioinformatics/RESULTS.md, hierarchicalAncestors, run 2026-11-04) shows that none of the Cbc substrate terms (GO:0015226, GO:1902603, GO:0015879, GO:0031460, GO:0015220), nor GO:0015418 or GO:0015651, sits under GO:0005275 or GO:0015837; carnitine and betaine transport sit under quaternary ammonium group transport (GO:0015697/GO:0015651). This is a lateral mis-placement rather than a true-but-broad ancestor, so the term is replaced by the correct sibling branch instead of being kept as non-core. The genes/human/SLC22A5 review keeps GO:0015837 on a carnitine transporter as correct but general; the difference from that precedent is deliberate and follows the OLS placement. This supersedes the batch-03 TreeGrafter re-review, which removed the row as a qualifier-only correction (PR #5954). The enables qualifier is also wrong for a permease subunit and is recorded as a source defect.

Proposed replacements: ABC-type quaternary ammonium compound transporting activity

Summary: CbcW is a multi-pass inner-membrane permease.

Reason: UniProt predicts six transmembrane helices and a cell-membrane location.

Summary: Correct activity of the CaiX-CbcWV complex that CbcW belongs to; the enables qualifier should be contributes_to.

Reason: The carnitine transporter activity is the right term for the complex: CaiX supplies carnitine selectivity and CbcWV the translocation path. The row is kept and the qualifier error recorded as a source defect, the convention used for the CaiX (Q9HTH6) and CbcV rows and for the BenB subunit in genes/ACIAD/benB; the core function records CbcW with contributes_to. This supersedes the batch-03 TreeGrafter re-review, which removed the row as a qualifier correction (PR #5954).

Summary: Derived mechanically from the amine transporter row; the Cbc substrates are not amines in GO.

Reason: Same lateral mis-placement as the GO:0005275 row (OLS4 query in cbcW-bioinformatics/RESULTS.md): carnitine, glycine betaine and choline transport are not under GO:0015837. The transport claim is replaced by the specific process terms already on this gene. The SLC22A5 review's KEEP_AS_NON_CORE for this term on a carnitine transporter differs from this call deliberately, following the OLS placement.

Proposed replacements: carnitine transmembrane transport choline transport glycine betaine transport

Summary: CbcW participates in CbcX-dependent choline uptake.

Reason: Characterized Pseudomonas CbcWV cores transport choline with CbcX; GO has no transmembrane child for choline transport.

Summary: Correct but less specific than plasma membrane.

Reason: CbcW is an integral inner-membrane protein; GO:0005886 is already on this gene.

Proposed replacements: plasma membrane

Summary: The shared CbcWV core supports glycine-betaine uptake with a cognate binding protein.

Reason: Pseudomonas Cbc systems transport betaine through the shared core with BetX or CbcX; GO has no transmembrane child for this process.

Summary: CbcW is the membrane subunit of a binding-protein-dependent ABC importer.

Reason: The Cbc importer depends on periplasmic binding proteins, which is GO:0055052, an is_a child of this term.

Proposed replacements: ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing

Summary: Correct but general.

Reason: GO:1902603 carnitine transmembrane transport is the supported is_a descendant already on this gene.

Proposed replacements: carnitine transmembrane transport

Summary: CbcW participates in CaiX-dependent carnitine import.

Reason: The CbcWV core is experimentally required for carnitine uptake in related Pseudomonas systems.