ccmF (PA1480, Q9I3N2) notes

Literature (own research, 2026-11-05)

System I cytochrome c maturation: CcmF with CcmH is the heme lyase; CcmF accepts heme from holo-CcmE PMID:19629033. E. coli CcmF is a b-type cytochrome and quinol:heme oxidoreductase PMID:19629033; PMID:19629033.
P. aeruginosa ccmF insertion mutant: milder pleiotropic phenotypes than ccmC PMID:18174132; reduced [Fe-S] clusters in both.
All five PseudoCAP IMP rows (pyoverdine, catalase, twitching, swimming, swarming) cite PMID:16824107 (Feissner et al. 2006, CcmABC/holo-CcmE release; abstract does not mention CcmF). Same mis-keying as on ccmC (genes/PSEAE/ccmC); re-key to PMID:18174132, PROBABLE (abstract-only).
Treatment follows the ccmC review: catalase REMOVE (CONFIRMED WRONG_TERM), pyoverdine and swimming MARK_AS_OVER_ANNOTATED, twitching and swarming REMOVE (PROBABLE).
PMID:16824107 and PMID:18174132 are abstract-only; full text not retrievable this session.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN009171456	GO:0016491 oxidoreductase activity	2	67 (36 taxa)	GO:0004096 catalase activity, IMP, PMID:16824107	INDIRECT-PHENOTYPE	Loss of catalase activity in a cytochrome c maturation mutant reflects heme supply to the heme catalases; CcmF is not a catalase. Also keyed to the wrong paper.	E. coli CcmF P33927 (GO:0016679 quinol:heme oxidoreductase, IDA PMID:19629033)	Yes; the E. coli seed directly supports an oxidoreductase activity, which is correct for CcmF

PseudoCAP defects: WRONG_TERM (catalase, CONFIRMED), WRONG_TERM (twitching, swarming; PROBABLE), WRONG_REFERENCE REPOINT PMID:16824107 -> PMID:18174132 (PROBABLE), WRONG_REFERENCE CHECK on swimming (SUSPECTED). No GO_CENTRAL defect: the IBD is right for the clade for a different reason than its PseudoCAP seed. The IBA row is MODIFIED to GO:0016679 for granularity. The ccmC plasma-membrane node (PTN000768541) is unaffected.

Action counts

ACCEPT 3, MODIFY 3, KEEP_AS_NON_CORE 1, MARK_AS_OVER_ANNOTATED 3, REMOVE 4.