id: Q2U1U6 gene_symbol: Q2U1U6 product_type: PROTEIN aliases: - AO090138000091 status: DRAFT taxon: id: NCBITaxon:510516 label: Aspergillus oryzae RIB40 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: - issue_type: TRUNCATED_GENE_MODEL status: CONFIRMED description: >- 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. evidence_types: - ORTHOLOG_COMPARISON - GENOMIC_SEQUENCE supported_by: - reference_id: file:ASPOR/Q2U1U6/Q2U1U6-bioinformatics/RESULTS.md supporting_text: '**Q2U1U6 is the C-terminal end of a ~408-aa protein.**' - reference_id: file:ASPOR/Q2U1U6/Q2U1U6-bioinformatics/RESULTS.md supporting_text: Q2U1U6 is a **truncated gene model** - reference_id: file:ASPOR/Q2U1U6/Q2U1U6-bioinformatics/RESULTS.md supporting_text: intronic ATG and omits exon 1. existing_annotations: [] references: - id: PMID:16372010 title: Genome sequencing and analysis of Aspergillus oryzae. findings: - statement: >- The A. oryzae RIB40 genome was sequenced and its genes, including AO090138000091, were predicted computationally from homology, ESTs and gene-finding software rather than from transcript-verified structures. supporting_text: >- Genes were predicted in the A. oryzae genome reference_review: relevance: LOW correctness: VERIFIED review_notes: >- Genome paper that is the source of the AO090138000091 gene model (cited in the UniProt entry). It says nothing about this locus specifically; used only for the provenance of the computational gene model. The earlier finding quoted only the paper's title; replaced with a quote from its methods. - id: UniProt:Q2U1U6 title: UniProt entry for Q2U1U6 findings: - statement: >- The protein contains a Chondroitin_lyas domain (IPR008929) and matches the Chondroitin AC/alginate lyase superfamily fold (SSF48230). supporting_text: >- InterPro; IPR008929; Chondroitin_lyas. - statement: >- The protein has a structural match to the chondroitin AC/alginate lyase superfamily. supporting_text: >- SUPFAM; SSF48230; Chondroitin AC/alginate lyase; 1. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- TrEMBL entry (PE 4, unreviewed). The only functional information is the fold-level IPR008929/SSF48230 signature; no Pfam, PANTHER or CAZy family is assigned. The protein name ("DNA, SC138") is a submitter placeholder. - id: file:ASPOR/Q2U1U6/Q2U1U6-hypotheses/prediction-glycoside-hydrolase/openscientist.md title: OpenScientist hypothesis report on the glycoside hydrolase prediction for Q2U1U6 findings: - statement: >- Among the four A. oryzae proteins with the IPR008929 signature, Q2U1U6 (134 aa) is the only short one; the others are about 400-450 aa. supporting_text: >- Q2U1U6 is the lone truncated outlier reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Independent computational report (InterPro, AlphaFold and UniProt queries). Its length-outlier observation is retained and is now explained by the gene-model analysis in Q2U1U6-bioinformatics/RESULTS.md (truncated model missing exon 1). Not used as support for any function; the 2026-10-21 re-review relies on its own sequence analysis. - id: file:ASPOR/Q2U1U6/Q2U1U6-deep-research-falcon.md title: Falcon deep research report for Q2U1U6 findings: - statement: >- No direct experimental characterization of Q2U1U6 was identified; functional inference rests entirely on domain architecture. supporting_text: >- no direct experimental characterization of this specific protein was identified in the scientific literature - statement: >- The Chondroitin_lyas domain is characteristic of polysaccharide lyases that cleave glycosaminoglycan chains by beta-elimination. supporting_text: >- Polysaccharide lyases containing the Chondroitin_lyas domain cleave glycosidic bonds through a beta-elimination mechanism, which is fundamentally different from the hydrolytic mechanism employed by glycoside hydrolases - statement: >- Aspergillus section Flavi species encode large CAZyme repertoires including polysaccharide lyases. supporting_text: >- species in Aspergillus section Flavi, including A. oryzae, encode abundant carbohydrate-active enzymes (CAZymes), averaging approximately 598 CAZymes per species, including numerous polysaccharide lyases involved in complex polysaccharide degradation reference_review: relevance: LOW correctness: UNVERIFIED review_notes: >- LLM-generated literature summary. It confirms the absence of experimental literature but argues by analogy to bacterial chondroitin lyases (substrates, secretion) without any phylogenetic link to this fungal protein, and does not notice the truncated gene model. Its GAG-substrate and secretion analogies are no longer used in the description or core functions. - id: file:ASPOR/Q2U1U6/Q2U1U6-bioinformatics/RESULTS.md title: Q2U1U6 gene-model check findings: - statement: >- Q2U1U6 corresponds to the C-terminal residues 280-408 of the 408-aa A. flavus ortholog A0A7U2MCM8 (128/129 identity). supporting_text: >- **Q2U1U6 is the C-terminal end of a ~408-aa protein.** - statement: >- The missing N-terminal exon is encoded upstream in the RIB40 genome and joined by a 65-nt GT-AG intron; the annotated start codon lies inside the intron. supporting_text: >- **A 65-nt GT...AG intron joins the two parts.** - statement: >- The full-length product has no PANTHER or Pfam family; its only signature is the fold-level chondroitin AC/alginate lyase superfamily. supporting_text: >- The full-length protein has no PANTHER family or Pfam family assignment; reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Reproducible analysis written for this re-review (gene_model_check.py, output in gene_model_check_output.txt). Establishes that the benchmark accession is a truncated gene model. core_functions: - molecular_function: id: GO:0016837 label: "carbon-oxygen lyase activity, acting on polysaccharides" description: >- 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. knowledge_gaps: - gap_statement: >- It is unknown whether the full-length AO090138000091 product has any polysaccharide lyase (or related epimerase) activity, and if so on which substrate; the protein is placed only at the fold level and lacks any family-level assignment linking it to characterized enzymes. boundary: >- The full-length ortholog carries a complete IPR008929/SSF48230 toroid domain; characterized members of this fold act on uronic-acid-containing polysaccharides. gap_kind: - BIOLOGY dark_aspect: MF_DARK - gap_statement: >- It is unknown whether the corrected two-exon transcript is expressed in A. oryzae RIB40 and whether the protein is secreted. boundary: >- Exon 1 and a canonical GT-AG intron are present in the genome; transcript and localization evidence have not been examined. gap_kind: - BIOLOGY dark_aspect: CC_DARK supported_by: - reference_id: UniProt:Q2U1U6 supporting_text: >- InterPro; IPR008929; Chondroitin_lyas. - reference_id: UniProt:Q2U1U6 supporting_text: >- SUPFAM; SSF48230; Chondroitin AC/alginate lyase; 1. - reference_id: file:ASPOR/Q2U1U6/Q2U1U6-bioinformatics/RESULTS.md supporting_text: >- **Q2U1U6 is the C-terminal end of a ~408-aa protein.** suggested_questions: - question: >- 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? - question: >- 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? - question: >- 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: - description: >- 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. experiment_type: transcript structure analysis - description: >- 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. experiment_type: biochemical assay - description: >- 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. experiment_type: computational structural analysis