A0A2G9RZF1

UniProt ID: A0A2G9RZF1
Organism: Aquarana catesbeiana
Review Status: DRAFT
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Gene Description

A0A2G9RZF1 is a gene prediction fragment from the fragmented draft genome assembly of Aquarana catesbeiana (American bullfrog). The 156-amino acid ORF (AB205_0007200) encodes a single CUB domain (residues 31-147), but scaffold KV928989 contains two additional consecutive ORFs (A0A2G9RZH1 with EGF+CUB domains, and A0A2G9RZI6 with CUB+EGF+CUB domains, the latter explicitly flagged as a fragment by UniProt) whose combined domain architecture (CUB-EGF-CUB-CUB-EGF-CUB) matches the C-terminal region of a tolloid-family metalloprotease (BMP-1 or TLL1). A 2024 chromosome-level assembly (GCF_042186555.1) with ~17,000-fold better contiguity encodes complete BMP-1 (XP_073478370.1, 1,020 aa, LG03) and TLL1 (XP_073462190.1, 1,005 aa, LG01), confirming the original draft produced fragmented gene models. The complete gene product is a tolloid-family metalloprotease with metalloendopeptidase activity. No experimental data exist for this protein (UniProt protein evidence level 4: Predicted).

Core Functions

A0A2G9RZF1 is almost certainly a gene prediction fragment from a poorly assembled draft genome, representing one CUB domain from a much larger (~1,000 aa) tolloid-family metalloprotease (BMP-1 or TLL1). The 156-amino acid ORF cannot be meaningfully annotated with a specific molecular function. GO:0005201 (extracellular matrix structural constituent) was previously hypothesized based on CATH FunFam classification to PCPE-1, but this was refuted by OpenScientist analysis on three grounds: (1) GO:0005201 describes structural ECM proteins (collagens, elastin), not CUB-domain interaction modules; (2) PCPE-1 real function is peptidase activator activity (GO:0016504, IDA), and individual CUB domains cannot perform PCPE-1 function (requires cooperative CUB1+CUB2 with >1,000-fold higher affinity than single domains); (3) genomic context shows three consecutive fragmented ORFs on scaffold KV928989 matching tolloid-like architecture, and a 2024 chromosome-level assembly (GCF_042186555.1) encodes complete BMP-1 (1,020 aa) and TLL1 (1,005 aa). The conservative MF assignment of protein binding reflects only that CUB domains are established protein-protein interaction modules; the actual function of the complete gene product would be metalloendopeptidase activity.

Molecular Function:
molecular_function
Cellular Locations:
Supporting Evidence:
  • file:AQUCT/A0A2G9RZF1/A0A2G9RZF1-hypotheses/core-function-1-go-0005201/openscientist.md
    [OpenScientist verdict: REFUTED. GO:0005201 is semantically inappropriate for CUB-domain proteins, the PCPE-1 FunFam evidence chain fails (PCPE-1 function is peptidase activator activity, individual CUB domains lose >1,000-fold affinity), and A0A2G9RZF1 is a gene prediction fragment from a fragmented genome assembly confirmed by a 2024 chromosome-level assembly encoding complete BMP-1 (1,020 aa) and TLL1 (1,005 aa)]
  • PMID:19801683
    only those containing both CUB1 and CUB2 were capable of enhancing BMP-1 activity and binding to a mini-procollagen substrate with nanomolar affinity. Both these properties were lost by individual CUB domains, which had dissociation constants at least three orders of magnitude higher
  • PMID:21954942
    CUB domains are 110-residue protein motifs exhibiting a Ξ²-sandwich fold and mediating protein-protein interactions in various extracellular proteins
  • file:AQUCT/A0A2G9RZF1/A0A2G9RZF1-uniprot.txt
    [UniProt record: CUB domain at residues 31-147; InterPro IPR000859 CUB_dom; Pfam PF00431 CUB; PANTHER PTHR24251 OVOCHYMASE-RELATED; protein existence level 4 (Predicted)]

References

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Suggested Questions for Experts

Q: Which complete tolloid-family gene does this fragment correspond to -- BMP-1 (XP_073478370.1 on LG03) or TLL1 (XP_073462190.1 on LG01)? A BLAST alignment of scaffold KV928989 against the chromosome-level assembly (GCF_042186555.1) would definitively resolve this. OpenScientist analysis confirmed A0A2G9RZF1 is a gene prediction fragment, but the specific gene identity remains undetermined.

Q: When will the UniProt proteome for Aquarana catesbeiana (UP000228934) be updated from the 2017 draft assembly to the 2024 chromosome-level assembly (GCF_042186555.1)? This update would supersede the fragment entries (A0A2G9RZF1, A0A2G9RZH1, A0A2G9RZI6) with complete gene models carrying appropriate metalloendopeptidase annotations.

Q: Does Aquarana catesbeiana have a genuine PCPE-1/PCOLCE1 ortholog separate from the tolloid-family metalloproteases? A reciprocal best BLAST of human PCPE-1 (Q15113) against the chromosome-level proteome would clarify whether the CATH FunFam classification to PCPE-1 reflects any real orthology relationship or is purely fold-level similarity.

Suggested Experiments

Experiment: Align scaffold KV928989 from the RCv2.1 draft assembly against the chromosome-level assembly (GCF_042186555.1) using BLAST or minimap2 to definitively map A0A2G9RZF1 to either BMP-1 (XP_073478370.1, LG03) or TLL1 (XP_073462190.1, LG01). This computational experiment would resolve the remaining ambiguity about gene identity.

Hypothesis: A0A2G9RZF1 is a fragment of a BMP-1 or TLL1 tolloid-family metalloprotease, not a standalone protein.

Type: bioinformatics

Experiment: Clone the full-length BMP-1 or TLL1 gene from Aquarana catesbeiana cDNA using the chromosome-level assembly as reference, express recombinantly, and assay metalloendopeptidase activity against procollagen or Chordin substrates. Compare with Xenopus Xolloid, the closest well-characterized amphibian ortholog.

Hypothesis: The complete tolloid-family metalloprotease corresponding to A0A2G9RZF1 has metalloendopeptidase activity and functions in procollagen processing or BMP signaling regulation.

Type: biochemistry

External Prediction Reviews

These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.

ProtNLM2 External predictions

View prediction review YAML Β· A0A2G9RZF1-protnlm-predictions-review.yaml Β· Review status: COMPLETE

A0A2G9RZF1 is a single-CUB fragment from a fragmented Aquarana catesbeiana draft gene model. The ProtNLM2 single-fertilization prediction is refuted for the sequence supplied to the model, because that sequence lacks the S1 protease domain required for an ovochymase-like egg-envelope protease; extracellular-region localization remains plausible but unresolved for the exact short accession.

Source documents: genes/AQUCT/A0A2G9RZF1/A0A2G9RZF1-uniprot.txt Β· genes/AQUCT/A0A2G9RZF1/A0A2G9RZF1-goa.tsv Β· publications/PMID_8510165.md Β· genes/AQUCT/A0A2G9RZF1/A0A2G9RZF1-ai-review.yaml Β· genes/AQUCT/A0A2G9RZF1/A0A2G9RZF1-hypotheses/core-function-1-go-0005201/openscientist.md Β· genes/AQUCT/A0A2G9RZF1/A0A2G9RZF1-hypotheses/prediction-ovochymase-fertilization/openscientist.md

Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.

GO:0007338 single fertilization GO_BP
NPI β€” Nonparalog incorrect Review score: 0/2
Prediction method: ProtNLM2 Β· Version: UniProt 2024_06 pilot
DOMAIN ARCHITECTURE MISMATCH
Review rationale: The target sequence is a 156-residue single-CUB ORF from the fragmented 2017 bullfrog assembly, not a complete CUB-only paralog whose subfamily should be read as independent evidence for loss of ovochymase activity. The existing curated review and its OpenScientist core-function audit found that adjacent KV928989 ORFs reconstruct a tolloid-like CUB-EGF-CUB-CUB-EGF-CUB region and that the 2024 chromosome-level assembly encodes complete BMP-1 and TLL1 metalloproteases, so this accession is best treated as a fragment of an extracellular tolloid-family protease. The fertilization prediction is still incorrect for the sequence supplied to ProtNLM2: the ovochymase audit shows the short accession lacks any S1 serine-protease domain and the His-Asp-Ser triad required for the egg-envelope protease activity underlying GO:0007338. This is therefore a gene-model/input-sequence failure rather than paralogous transfer to a genuine stand-alone CUB protein.
Supporting Evidence:
GO:0005576 extracellular region GO_CC
UNC β€” Uncertain Review score: 1/2
Prediction method: ProtNLM2 Β· Version: UniProt 2024_06 pilot
Review rationale: The sequence contains a nearly complete CUB domain at residues 31-147, and the comparative analysis defining CUB domains places this module in extracellular proteins with diverse functions. The existing curated review also accepts extracellular region for the draft fragment because a CUB domain from a tolloid-family protease is expected to act extracellularly. The focused ovochymase audit nevertheless found no signal-peptide confirmation for the exact 156-residue UniProt entry, and the TrEMBL record has no FT SIGNAL feature. The broad extracellular-region prediction is therefore plausible and aligned with the main review's location inference, but still UNC for the exact short accession rather than confirmed from an experimentally supported mature product.
Supporting Evidence:

Deep Research

Falcon

(A0A2G9RZF1-deep-research-falcon.md)

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OpenScientist

(A0A2G9RZF1-hypotheses/core-function-1-go-0005201/openscientist.md)

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OpenScientist

(A0A2G9RZF1-hypotheses/prediction-ovochymase-fertilization/openscientist.md)

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