Q2U1U6

UniProt ID: Q2U1U6
Organism: Aspergillus oryzae RIB40
Review Status: DRAFT
Aliases:
AO090138000091
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Gene Description

Q2U1U6 is the TrEMBL translation of locus AO090138000091 on chromosome 6 of Aspergillus oryzae RIB40, an uncharacterized protein whose only signature is the chondroitin AC/alginate lyase fold (InterPro IPR008929, SUPFAM SSF48230), an alpha/alpha-toroid scaffold shared by bacterial polysaccharide lyases and related glycosaminoglycan-modifying enzymes. The annotated product (134 aa) is a truncated gene model: it is identical to the C-terminal residues 280-408 of the 408-aa ortholog in A. flavus, and the missing N-terminal exon is present in the RIB40 genome immediately upstream, joined by a 65-nt intron inside which the annotated start codon lies. The full-length product of this locus is therefore expected to be a ~408-aa protein carrying a complete lyase-like toroid domain. No family-level (Pfam, PANTHER, CAZy) assignment and no experimental data exist for this protein or its fungal orthologs, so a polysaccharide lyase activity is a fold-level prediction, and its substrate, localization and biological role are unknown.

Gene Model Issues

The protein sequence of this entry may not correspond to a single real gene product (for example, two neighbouring genes joined into one model, or a truncated model). Read the name, features and annotations of the entry with this in mind.

TRUNCATED GENE MODEL CONFIRMED ORTHOLOG COMPARISONGENOMIC SEQUENCE

The 134-residue model starts at an ATG inside an intron and omits exon 1. The RIB40 genome encodes the missing ~279 N-terminal residues immediately upstream, joined by a 65-nt GT...AG intron, and the annotated product is identical to the C-terminal residues 280-408 of the 408-residue A. flavus ortholog. Functional statements apply to the full-length ~408-residue product, not to this translation.

Supported by:

Core Functions

Fold-level prediction only. The full-length product of AO090138000091 (~408 aa, once the missed N-terminal exon is restored) carries a complete chondroitin AC/alginate lyase alpha/alpha-toroid domain, a fold whose characterized members cleave uronic-acid-containing polysaccharides by beta-elimination. No Pfam, PANTHER or CAZy family places this fungal protein with any characterized lyase, so the substrate is unknown and the activity itself is unverified. The 134-aa Q2U1U6 translation contains only the last third of the domain and is not expected to be catalytically competent as annotated.

Supporting Evidence:
  • UniProt:Q2U1U6
    InterPro; IPR008929; Chondroitin_lyas.
  • UniProt:Q2U1U6
    SUPFAM; SSF48230; Chondroitin AC/alginate lyase; 1.
  • file:ASPOR/Q2U1U6/Q2U1U6-bioinformatics/RESULTS.md
    **Q2U1U6 is the C-terminal end of a ~408-aa protein.**

References

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Suggested Questions for Experts

Q: Should the AO090138000091 gene model (and UniProt Q2U1U6) be corrected to the two-exon ~408-aa structure supported by the A. flavus ortholog A0A7U2MCM8 and the RIB40 genome sequence?

Q: Does the full-length fungal protein belong to a defined polysaccharide lyase family (e.g. a CAZy PL family) when assessed with family-level HMMs rather than the superfamily signature alone?

Q: Is the 745-aa A. oryzae var. brunneus model A0ABQ6LHX9, which fuses this lyase-fold protein to an upstream beta-lactamase-related domain, a merged gene model?

Suggested Experiments

Experiment: RNA-seq read mapping or RT-PCR across the predicted 65-nt intron (AP007170.1:187011-187075) to confirm the two-exon transcript structure.

Hypothesis: AO090138000091 is transcribed as a two-exon mRNA encoding a ~408-aa protein.

Type: transcript structure analysis

Experiment: Recombinant expression of the corrected full-length protein and activity screens on uronic-acid-containing polysaccharides (alginate, chondroitin sulfate, hyaluronan, heparosan, ulvan), monitoring unsaturated product formation at 232 nm.

Hypothesis: The full-length protein is a polysaccharide lyase acting on one of these substrates.

Type: biochemical assay

Experiment: Structure-based search (e.g. Foldseek) of the AlphaFold model of the full-length ortholog against characterized lyases, followed by conservation analysis of the His/Tyr catalytic positions.

Hypothesis: The fungal toroid domain retains the catalytic residues of a specific characterized polysaccharide lyase family.

Type: computational structural analysis

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· Q2U1U6-protnlm-predictions-review.yaml Β· Review status: COMPLETE

Q2U1U6 (locus AO090138000091) is a 134-residue TrEMBL translation whose only signature is the chondroitin AC/alginate lyase alpha/alpha-toroid fold (IPR008929, SSF48230). It is a truncated gene model covering the C-terminal residues 280-408 of a ~408-aa fungal ortholog, so the full-length product carries a complete lyase-like toroid domain. The gene review assigns a fold-level, unverified polysaccharide lyase activity; no experimental data, family-level (Pfam, PANTHER, CAZy) assignment or literature exist for this protein or its fungal orthologs. Neither polysaccharide catabolism nor O-glycosyl hydrolase activity is established.

Source documents: genes/ASPOR/Q2U1U6/Q2U1U6-uniprot.txt Β· genes/ASPOR/Q2U1U6/Q2U1U6-goa.tsv Β· genes/ASPOR/Q2U1U6/Q2U1U6-ai-review.yaml Β· genes/ASPOR/Q2U1U6/Q2U1U6-bioinformatics/RESULTS.md Β· genes/ASPOR/Q2U1U6/Q2U1U6-hypotheses/prediction-glycoside-hydrolase/openscientist.md

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

GO:0000272 polysaccharide catabolic process GO_BP
UNC β€” Uncertain Review score: 1/2
Prediction method: ProtNLM2 Β· Version: UniProt 2024_06 pilot
Review rationale: Scored for the 134-residue Q2U1U6 translation, which is a truncated gene model: it corresponds only to residues 280-408 of the ~408-aa full-length product (A. flavus ortholog A0A7U2MCM8, 128/129 identity), because the AO090138000091 model starts at an ATG inside a 65-nt intron and omits the ~279-codon first exon. In the full-length product the chondroitin AC/alginate lyase alpha/alpha-toroid domain (IPR008929, SSF48230, Gene3D 1.50.10.100) spans residues ~62-371, so this accession carries only roughly the last third of the toroid and is unlikely to be a competent lyase. That does not refute the process term: no participation mechanism in polysaccharide catabolism is known for this gene even at full length (the lyase activity is a fold-level, unverified inference with unknown substrate, no Pfam/PANTHER/CAZy family, no GOA annotations, no literature), so the process cannot be shown to depend solely on the missing part of the fold. A non-catalytic structural or binding contribution by the fragment is neither shown nor excluded. With no positive evidence for or against participation, the prediction is uncertain.
Supporting Evidence:
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds GO_MF
NPI β€” Nonparalog incorrect Review score: 0/2
Prediction method: ProtNLM2 Β· Version: UniProt 2024_06 pilot
DOMAIN ARCHITECTURE MISMATCH
Review rationale: The protein's only signature is the chondroitin AC/alginate lyase alpha/alpha-toroid fold (IPR008929, SSF48230), whose characterized members cleave uronic-acid-containing polysaccharides by beta-elimination rather than hydrolysis. The full-length product of the truncated gene model has no Pfam, PANTHER or CAZy glycoside hydrolase family assignment, and the re-reviewed gene's core function is a fold-level carbon-oxygen lyase activity acting on polysaccharides. No experimental evidence or literature exists for any glycosidase activity. The O-glycosyl hydrolase prediction transfers a hydrolytic activity onto a lyase fold and is discordant with the only available domain evidence.
Supporting Evidence:

Deep Research

Falcon

(Q2U1U6-deep-research-falcon.md)

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OpenScientist

(Q2U1U6-hypotheses/prediction-glycoside-hydrolase/openscientist.md)

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πŸ“š Additional Documentation

Notes

(Q2U1U6-notes.md)

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Bioinformatics Results

(RESULTS.md)

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πŸ“„ View Raw YAML

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