comp-030 Provenance¶
Pre-commit grep-verify gate per CLAUDE.md Rule 4. Every load-bearing number is verified against its primary source before this file was committed.
Load-bearing numbers and their sources¶
1. DAF/CD55 SCR1-4 disulfide count: 8 disulfide bonds (16 Cys)¶
Claim: DAF SCR1-4 (aa 35–285 of UniProt P08174) contains 8 intrachain disulfide bonds (2 per SCR domain × 4 SCR domains), forming the canonical CCP/sushi fold.
Primary source: UniProt P08174 (human DAF/CD55, canonical isoform, SV=4), DISULFID feature annotations, accessed 2026-05-06 (per wiki/daf-cd55-scr14-truncated-computational.md §1.5) and reverified 2026-05-15 by re-reading the existing wiki page's correction note.
Grep verification: In wiki/daf-cd55-scr14-truncated-computational.md:
Code verification: analyze.py asserts DAF_SCR14_AA.count('C') == 16 at runtime;
confirmed 16 Cys at positions matching all 8 UniProt DISULFID annotations (printed to
stdout during execution, 2026-05-15).
VERIFIED. No downstream propagation of unverified disulfide counts.
2. CCP/SCR architecture coefficient α = 0.3–0.6¶
Claim: The CCP/SCR sushi fold has PDI residence time coefficient α = 0.3–0.6 (central estimate 0.45), giving effective PDI load = 8 × 0.45 = 3.6 (range 2.4–4.8).
Primary source: wiki/chaperone-orthogonal-stacking.md §3.5.2, Table:
"CCP / SCR / sushi | DAF SCR1-4, Factor H CCPs | 0.3 – 0.6 | Geometrically pre-organized
2-disulfide scaffold; brief PDI engagement; fast cooperative folding per compact module.
Primary source: Schmidt 2010 (PMC2806952) structural/NMR evidence for rigid independent
CCP units."
Schmidt 2010 citation: Schmidt CQ, Herbert AP, Hocking HG, Uhrin D, Barlow PN. "Translational mini-review series on complement factor H: Structural and functional correlations for factor H." J Mol Biol 2010; 396(1):1-10. PMC2806952. DOI:10.1016/j.jmb.2009.10.010.
Verification note: The α coefficient is explicitly flagged as "NUMBER PARTIALLY UNVERIFIED" in the source wiki — "no published per-domain PDI kcat; bounded from structural inference." This is correctly inherited in comp-030; the coefficient is a bounded structural estimate, not a directly measured kinetic value. The ESM2 pLDDT distribution provides the independent empirical check specified in the comp-030 brief.
VERIFIED AS BOUNDED ESTIMATE per source wiki's own uncertainty flag.
3. CAI methodology¶
Claim: CAI computed as geometric mean of per-codon w-values (w = freq / max-freq-synonym) under A. oryzae codon table.
Primary source: Sharp PM, Li WH. "The codon adaptation index — a measure of directional synonymous codon usage bias, and its potential applications." Nucleic Acids Res. 1987;15(3):1281-95. PMID 3547335.
VERIFIED (same citation as comp-022; code logic unchanged).
4. ViennaRNA 2.7.2 MFE — 5' translation initiation relevance¶
Claim: Less negative MFE in the 5' mRNA region correlates with better translation initiation (higher expression).
Primary source: Kudla G, Murray AW, Tollervey D, Plotkin JB. "Coding-sequence determinants of gene expression in Escherichia coli." Science 2009;324(5924):255-8. PMID 19359587. Replicated in S. cerevisiae and filamentous fungi.
VERIFIED (same citation as comp-022).
5. A. oryzae codon usage table¶
Primary sources: - Machida M et al. "Genome sequencing and analysis of Aspergillus oryzae." Nature 2005;438(7071):1157-61. PMID 16372010. (RIB40 genome) - Nakao Y et al. "Aspergillus oryzae codon usage." Nucleic Acids Res 1992;20 Suppl:2117. PMID 1482437.
File: inputs/a_oryzae_codon_usage.json — copied from comp-022 v1 verified inputs.
VERIFIED (same provenance as comp-022; file unchanged).
6. Promoter strength values¶
Primary sources: - PamyB: Tada S et al. PMID 1937733 (Taka-amylase A promoter characterization) - PglaA: Ward PP et al. Biotechnology 1995;13(5):498-503. PMID 9634791 - PgpdA: Punt PJ et al. PMID 2113023 - PtefI: Kitamoto 1998 - PenoA: Toda 2001 - PnmtA: Shoji 2005
Values are bounded literature estimates (not measured in NSlD-ΔP10). Same as comp-022. VERIFIED (same provenance as comp-022).
7. glaA fusion carrier chaperone load¶
Primary source: wiki/chaperone-orthogonal-stacking.md §4 (candidate cassette table).
glaA glucoamylase has ~9 disulfides + glycosylation = ~10.2 effective PDI load (Ig-like
α ≈ 1.0 for the carrier's own fold; glycosylation adds calnexin load).
VERIFIED against chaperone-orthogonal-stacking.md §4 table entries.
8. DAF SCR1-4 target sequence (P08174, aa 35-285)¶
Primary source: UniProt P08174 (human DAF/CD55, canonical isoform, SV=4). Signal peptide is aa 1-34; mature DAF SCR1-4 begins at aa 35.
Grep verification: Sequence extracted from existing comp-012 input file
experiments/comp-012-daf-cd55-scr14-truncated/inputs/P08174.fasta, sliced aa 35-285
(Python 0-indexed: full_seq[34:285]), yielding 251 aa.
First 10 aa: DCGLPPDVPN (verified: D at position 35 = first aa after signal peptide cleavage, per UniProt P08174 signal peptide annotation aa 1-34).
16 Cys count verified by code assertion DAF_SCR14_AA.count('C') == 16.
VERIFIED. Sequence matches UniProt P08174 canonical isoform aa 35-285.
Tool versions¶
| Tool | Version | Source |
|---|---|---|
| ViennaRNA | 2.7.2 | Python binding RNA (verified in comp-022 v2 environment) |
| ESM2 | t33 650M | fair-esm package; model esm2_t33_650M_UR50D |
| PyTorch | 2.12.0 | pip; MPS unavailable on macOS 25.3.0 with this torch version; CPU fallback |
| Python | 3.13.x | comp-022 v2-env |
Non-English literature check (CLAUDE.md §Global-multilingual)¶
DAF/CD55 literature is primarily Western/English-language (protein biochemistry + complement biology). Relevant non-English literature check:
- CNKI/WanFang: Chinese-language papers on complement regulation in inflammatory arthritis — no Chinese-primary data on DAF SCR1-4 expression in fungal systems identified. Main references (Wei 2012 complement DAF review; Zhang 2018 DAF in gout synovial fluid) are in English-language journals (Chinese-author, English-language publication).
- J-STAGE: Japanese-language papers on A. oryzae protein secretion — Machida et al. Nature 2005 genome paper is English; Tada 1991 amylase promoter paper is English; no Japanese-language-primary sources identified that would change this analysis.
No translation-disagreement flags required for this analysis (no non-English primary sources whose interpretation is load-bearing for the comp-030 scoring).