CG30288 (Q8IRK6): evidence and ProtNLM claim review

CG30288 is a predicted secreted S1-family serine endopeptidase. Its 282-residue sequence has an N-terminal signal peptide and retains the annotated histidine-aspartate-serine catalytic triad. Proteolytic potential is supported, while its preferred substrate and physiological role remain unresolved.

Exact input: Q8IRK6, 282 residues. The accession was fetched explicitly with the gene-directory alias; no canonical-sequence substitution is made.

Raw emitted predictions: CG30288-predictions-source.json. Source features: CG30288-uniprot.txt, with an exact extraction in CG30288-sequence-evidence.json.

Sequence and domain evidence

These are sequence/domain observations or explicitly named feature predictions, not measurements of biological function. ARBA assertions and ProtNLM-derived UniProt names are not counted as validation.

DR   InterPro; IPR009003; Peptidase_S1_PA.
DR   InterPro; IPR001314; Peptidase_S1A.
DR   InterPro; IPR051487; Ser/Thr_Proteases_Immune/Dev.
DR   InterPro; IPR001254; Trypsin_dom.
DR   InterPro; IPR033116; TRYPSIN_SER.
FT   SIGNAL          1..23
FT                   /evidence="ECO:0000256|SAM:SignalP"
FT   DOMAIN          43..275
FT                   /note="Peptidase S1"
FT                   /evidence="ECO:0000259|PROSITE:PS50240"
FT   ACT_SITE        83
FT                   /note="Charge relay system"
FT                   /evidence="ECO:0000256|PROSITE-ProRule:PRU00274"
FT   ACT_SITE        132
FT                   /note="Charge relay system"
FT                   /evidence="ECO:0000256|PROSITE-ProRule:PRU00274"
FT   ACT_SITE        225
FT                   /note="Charge relay system"
FT                   /evidence="ECO:0000256|PROSITE-ProRule:PRU00274"

At the annotated catalytic positions, direct indexing of the exact sequence gives: H83, D132, S225. These positions come from PROSITE features, not a new alignment; no substrate preference or assay result is inferred.

ProtNLM claims

The snapshot emits names and location/keyword statements, with no GO or EC prediction for this target. Each actual statement is assessed below; no GO term has been substituted for it. Categories follow the function-prediction rubric, with nonspecific “uncharacterized” names marked UNC because they contain no testable function. CNN records an independently supported existing annotation; it does not assert a particular training-set composition.

Kind	Verbatim emitted statement	Assessment	Evidence and limitation
Name	Peptidase S1 domain-containing protein	CNN	The peptidase S1 domain at residues 43-275 is independently supported by PROSITE PS50240 and InterPro IPR001254. The name is a defensible structural assignment without substrate specificity.
Location	Secreted (SL-0243)	CNN	The predicted cleavable SignalP signal peptide and absence of a retained transmembrane segment support secretion; this is consistent with the existing phylogenetically curated extracellular annotation.

Literature evidence

PMID:30367934(https://pubmed.ncbi.nlm.nih.gov/30367934/): “The SP-related sequences in each species were divided into SPs or SPHs based on the presence or absence of the His-Asp-Ser catalytic triad”

Annotation decisions

GO:0004252 serine-type endopeptidase activity (IBA): ACCEPT. The exact sequence contains the annotated H83 D132 S225 triad in its S1 domain; the IBA is consistent with this intact catalytic architecture.
GO:0004252 serine-type endopeptidase activity (IEA): ACCEPT. PROSITE identifies an S1 domain with the retained annotated catalytic residues H83 D132 S225. This does not establish the narrower chymotrypsin substrate preference.
GO:0004252 serine-type endopeptidase activity (ISM): ACCEPT. PMID:30367934 classifies Drosophila serine proteases using the H-D-S triad and gene models. The exact source retains the annotated catalytic triad; no biochemical substrate specificity is inferred.
GO:0005576 extracellular region (IBA): ACCEPT. SignalP predicts a cleavable signal peptide at residues 1-23 and no retained transmembrane segment is annotated. This architecture supports the curated IBA extracellular location.
GO:0006508 proteolysis (IBA): ACCEPT. The intact S1 catalytic architecture supports broad proteolysis; the physiological substrate and tissue context remain unknown.
GO:0006508 proteolysis (IEA): ACCEPT. A retained H-D-S triad supports a catalytic rather than merely fold-homologous S1 protein.
GO:0008233 peptidase activity (IEA): MODIFY. The S1 domain and annotated H-D-S triad support serine-type endopeptidase activity.
GO:0016787 hydrolase activity (IEA): MODIFY. S1 catalytic architecture supports serine-type endopeptidase activity.

Research provenance

Genuine external literature research is requested through the repository Falcon wrapper, with perplexity-lite configured as fallback. Provider output is retained separately as CG30288-deep-research-<provider>.md; its source leads are checked against the underlying publications and exact sequence record.

2026-10-21 — Full re-review, independent of the ProtNLM2 predictions

Identity: the benchmark accession Q8IRK6 is the only UniProt product of CG30288 (FBgn0050288, SP225): 282 aa, sequence version 2, complete. It is not a fragment, an isoform or an alternative gene model. The signal peptide, propeptide, full S1 domain (43-275) and all three catalytic residues are present.

New sequence checks are in CG30288-bioinformatics/sequence_features_rereview.py and RESULTS-rereview.md, both new files:
- The triad His83/Asp132/Ser225 is intact, with Ser225 in the GDSGGP motif.
- Position 189 of the S1 pocket (chymotrypsinogen numbering) is Asp219. This predicts trypsin-like (Arg/Lys) P1 specificity. The UniProt name "Chymotrypsin"/EC 3.4.21.1 is a PROSITE-ProRule assignment and is not supported.
- The activation site is Arg42-|-Ile43 (IDGG), which predicts activation by a trypsin-like protease.
- The propeptide is only 19 residues, so there is no clip domain. This contradicts the ARBA-only statement "CLIP subfamily", and the Falcon deep-research framing of CG30288 as a CLIP protease is wrong on architecture. The SP (not cSP) name in PMID:30367934 agrees.

Phylogeny: PANTHER 19.0 places CG30288 in PTHR24256:SF546 (MIP11562P-RELATED). That subfamily contains only Drosophila proteins: CG30288, CG30289 (Q8IRK5, the neighbouring gene), CG30414 (C5WLM7) and SPH158 (Q9VWD8), none of them characterized. All three IBAs (GO:0004252, GO:0005576, GO:0006508) come from the deep node PTN001207268, which is seeded by easter (FB:FBgn0000533, SF527), human tryptases and mouse mast-cell proteases among others. PAINT placed IKR NOT GO:0004252 losses on several SPH clades, and CG30288 is not under any of them. That agrees with its retained triad. No subfamily-specific function (Toll activation, as for easter) is transferred, because easter is in a different subfamily and is a CLIP protease.

The family review interpro/panther/PTHR24256/PTHR24256-review.yaml lists CG30288 under "Benchmark members without resolved subfamily placement". This is not a disagreement: the PANTHER placement is SF546, and the review does not resolve subfamilies.

Literature: no gene-specific study. The deep research also found none.

Actions changed from the previous review: none flipped. Reasons were rewritten around the PAINT node and loss nodes, the chymotrypsin EC was flagged as unsupported, and the supporting quotes were trimmed to ones relevant to each row. The description and core function were rewritten: single-domain, trypsin-like, Drosophila-specific subfamily.

Modules: no module under modules/ mentions CG30288 or PTHR24256.