ccoP1

Summary: True for this leaf as a contribution to cbb3 oxidase activity, but the PTN002435498 node is a broad c-type cytochrome clade and rests only on the two P. aeruginosa CcoP rows.

Reason: CcoP1 is a subunit of the cbb3-1 oxidase (TIGR00782 ccoP, FixP_N plus two cytochrome c domains), so the activity belongs to the complex it is part of; core_functions records it as contributes_to. Q9I3G5 in its own WITH/FROM marks one of the two seeds, which is expected. The node is another matter. Its 32 leaves include soluble cytochromes c4 (P. aeruginosa cc4 P00106, Neisseria, Vibrio, Shewanella, Xanthomonas), cytochromes c552/c554, the bc1-complex cytochrome c subunit QcrC of M. tuberculosis and Streptomyces, and PvcD; none of these is a cytochrome c oxidase subunit. Both seeds are the same operon-level PseudoCAP IMP, so the IBD does not stand on independent evidence (GO_CENTRAL defect below, recorded once for this node; ccoP2 cross-references it).

Summary: Comolli and Donohue 2004 compared the two cbb3 isoforms; loss of cbb3-1 affected growth at high aeration. The same IMP is on all eight cbb3 subunits.

Reason: The claim that CcoP1 is part of the cbb3-1 cytochrome c oxidase is right and is the gene's core role, so the term is accepted. The qualifier is not. The abstract describes loss of each oxidase isoform, not a ccoP-specific mutant, and same-day PseudoCAP rows apply the identical IMP to CcoN, CcoO, CcoQ and CcoP of both operons. CcoP feeds electrons to the catalytic CcoN subunit, so it contributes to the activity rather than enabling it alone; filed as a qualifier defect at PROBABLE (abstract only).

Summary: The iron of CcoP is heme iron, already captured by heme binding.

Reason: The cytochrome c class I mapping adds iron ion binding, but CcoP binds iron only as heme c, covalently attached to CXXCH motifs; heme binding (GO:0020037) is the informative term and is already annotated.

Summary: Inner (plasma) membrane subunit of the cbb3 oxidase.

Reason: Two predicted N-terminal TM helices anchor the protein; the cbb3 oxidase is an inner-membrane complex.

Summary: Correct but general; CcoP works in the aerobic electron transport chain.

Reason: As an electron-transfer subunit of a terminal oxidase, CcoP acts in the aerobic electron transport chain (GO:0019646), which is part_of oxidative phosphorylation.

Proposed replacements: aerobic electron transport chain

Summary: CcoP's own molecular activity, electron transfer by its two c-type hemes.

Reason: Two cytochrome c domains with heme c binding sites; CcoP relays electrons from donor cytochromes to CcoO and CcoN.

Summary: Binds two heme c groups.

Reason: The heme c cofactors are the redox centres of the subunit; the record annotates the heme c binding residues from the PIRSR rule.

Summary: Inferred from the oxidase MF; proton pumping is done by the complex at the CcoN subunit.

Reason: The cbb3 complex pumps protons, and CcoP as a subunit takes part in the complex's electron flow, but CcoP itself has no proton channel. Kept as non-core participation through the complex.