sec11

Summary: The InterPro S26 peptidase domains correctly identify Q7RY44 as a catalytic serine endopeptidase, a mechanistic claim that complements the substrate-specific signal peptidase rows.

Reason: GO:0009003 signal peptidase activity is not an is_a descendant of GO:0004252; both terms are endopeptidase-activity children that describe orthogonal features of Sec11 catalysis. Q7RY44 carries the S26B/SPASE_I signatures and the conserved Ser/His/Asp active-site residues, so the serine-type endopeptidase assertion is retained alongside the exact signal peptidase activity rows.

Summary: The yeast ortholog transfer is consistent with Sec11 acting at the ER membrane but is too broad beside the more precise ER membrane rows.

Reason: Sec11 proteins are ER membrane components of the eukaryotic signal peptidase complex. GO:0005783 is true for Q7RY44 but is only a broad parent of the accepted endoplasmic reticulum membrane location already asserted in this review.

Summary: PTN000086750 places signal peptidase complex membership at the eukaryotic Sec11 ancestor, which cleanly covers fungal sec11.

Reason: Q7RY44 belongs to PTHR10806:SF6 and is an ortholog of budding yeast SEC11. The PAINT curator placed signal peptidase complex at the Eukaryota node, not at the full bacterial/archaeal/eukaryotic root, matching the eukaryote-specific ER signal peptidase complex architecture.

Summary: The automatic EnsemblFungi transfer from budding yeast SEC11 agrees with the PAINT eukaryotic-node placement of Sec11 in the ER signal peptidase complex.

Reason: Budding yeast SEC11 is the same PTHR10806:SF6 fungal Sec11 subfamily as Neurospora Q7RY44, and biochemical yeast studies establish that Sec11 is a signal peptidase complex subunit. There is no evidence for loss or relocalization of this conserved complex role in N. crassa sec11.

Summary: The UniProt SubCell mapping is consistent with Q7RY44 being an ER membrane Sec11 signal peptidase subunit.

Reason: Q7RY44 has an N-terminal signal-anchor helix and belongs to the eukaryotic ER signal peptidase complex catalytic-subunit family, making ER membrane the expected functional location.

Summary: Manual transfer of ER membrane localization from budding yeast SEC11 is appropriate for the Neurospora ortholog.

Reason: The fungal Sec11 proteins share the same catalytic Sec11 subfamily and type II membrane topology. Nothing in Q7RY44 suggests a compartment switch away from the ER membrane.

Summary: The root PTN000086749 IBA deliberately asserts only generic peptidase activity across a family that spans bacterial, archaeal, and eukaryotic signal peptidases.

Reason: Peptidase activity is true for Q7RY44, but the accepted signal peptidase activity rows are the informative molecular-function assertion for this gene. The broad PAINT placement is not a propagation error: PTN000086749 is the full PTHR10806 root and therefore cannot safely assert the eukaryotic ER signal peptidase complex context.

Summary: The automated UniProt/InterPro assertion is biologically correct but redundant with accepted signal peptidase activity.

Reason: Q7RY44 is specifically a signal peptidase rather than an unclassified peptidase. Since signal peptidase activity is retained, the generic peptidase row adds no useful specificity.

Summary: EC 3.4.21.89 signal peptidase I activity is the expected specific molecular function of the Q7RY44 Sec11 catalytic subunit.

Reason: Although the ARBA association rule alone is not independent evidence, signal peptidase activity is supported by the curated Sec11 family assignment, the conserved active-site architecture, the yeast SEC11 ISS transfer, and the eukaryotic PAINT complex/process placement.

Summary: Manual transfer of signal peptidase activity from budding yeast SEC11 is appropriate for Neurospora Q7RY44.

Reason: Neurospora Q7RY44 and S. cerevisiae SEC11 are close fungal members of PTHR10806:SF6, the PTHR10806 subfamily that retains Sec11 catalytic subunit sequence length, topology, and active-site residues. The yeast evidence for SEC11 therefore transfers to the Neurospora ortholog.

Summary: The S26B family correctly indicates that Q7RY44 is membrane associated, but the accepted ER membrane rows are the informative location.

Reason: Sec11 is a single-pass ER membrane subunit of the signal peptidase complex. The bare membrane annotation is true but uninformative beside the accepted endoplasmic reticulum membrane annotation.

Summary: Cleaving signal peptides after ER engagement does not mean Sec11 directs substrates to the ER.

Reason: Sec11 catalyzes signal peptide cleavage as nascent proteins are translocated at the ER membrane. The protein targeting to ER term instead describes directing proteins toward the ER using targeting signals, which is executed by SRP/Sec61 and Sec62/Sec63 targeting and translocation machinery rather than by the SPC catalytic subunit. The EnsemblFungi row therefore transfers a pathway-level yeast annotation that is too far upstream for sec11 itself.

Summary: The Eukaryota PTN000086750 IBA links Sec11 to protein maturation by ER signal peptide cleavage but should be refined to the live protein processing term for the SPC reaction.

Reason: Signal peptide removal is a proteolytic maturation step for secretory and membrane proteins, and PAINT correctly restricts this process assertion to eukaryotic Sec11 proteins in the ER signal peptidase complex rather than placing it at the full PTHR10806 root. GO:0051604 is broader than the signal-peptide cleavage step; after obsoletion of GO:0006465 signal peptide processing, GO:0016485 protein processing is the live process term that captures SPC proteolysis.

Proposed replacements: protein processing

Summary: The automated protein maturation row is consistent with Sec11's conserved signal peptide cleavage activity but is one level broader than the live SPC process term.

Reason: Q7RY44 catalyzes cleavage of signal peptides from nascent proteins in the ER signal peptidase complex. That cleavage is a direct protein maturation step, unlike the upstream protein targeting to ER process, and the InterPro:IPR001733/InterPro:IPR019533 sources specifically track the signal-peptidase family. GO:0016485 protein processing is the live process term for this proteolytic SPC reaction.

Proposed replacements: protein processing