STRC Research

STRC OTOA Paralog Phase1A Sequence Audit

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STRC OTOA Paralog Phase 1A Sequence Audit

Human STRC (UniProt Q7RTU9, 1775 aa) and OTOA (UniProt Q7RTW8, 1153 aa) share 28.3% global identity and 45.7% BLOSUM62 similarity over 1126 ungapped residues — a real paralog signal. The mini-STRC window (700–1775) retains 29.8% local identity against OTOA. The C-terminal ARM-repeat core (STRC 1603–1770) hits 33.8% identity over 148 residues, mapped to a near-continuous OTOA stretch (977–1136) — the ARM region is more conserved than the average protein, the classic paralog-by-function signature. Two of the four pharmacochaperone pocket anchors are identically conserved (F1646→F1014, E1659→E1027); the other two (K1141, G1645) fall in alignment gaps — the druggable sub-pocket is STRC-specific. Gate passed. Proceed to Phase 1B structural superposition.

Correction log

Phase 1A initial run used Q7RTW9 — that is NMD3B_HUMAN (NMDA receptor 3B), not OTOA. Caught when the canonical OTOA AF DB entry returned 404 for Q7RTW9. The correct OTOA accession is Q7RTW8 (OTOAN_HUMAN, 1153 aa). Numbers above are the corrected run; the script file now hard-codes Q7RTW8.

Method

  1. Fetched canonical FASTA + annotation JSON for STRC (Q7RTU9) and OTOA (Q7RTW8) from UniProt REST.
  2. Global Needleman–Wunsch alignment, BLOSUM62 matrix, gap open −11, extend −1 (Biopython PairwiseAligner).
  3. Local alignments: (a) mini-STRC window 700–1775, (b) ARM-repeat span 1603–1770, both against full OTOA.
  4. Sliding-window local alignment: 50-aa windows, step 20, 87 windows across STRC → OTOA.
  5. Anchor-residue projection: K1141, G1645, F1646 (pharmacophore triangle) + E1659 (Misha’s mutation) mapped through the global alignment to OTOA.

Deterministic. No stochastic components.

Results

Global metrics

MetricValue
STRC length1775 aa
OTOA length1153 aa
Global score (BLOSUM62)−158.0
Matched (ungapped) residues1126
Identity28.33%
Similarity (BLOSUM62 positive)45.74%

Region-specific local alignments

RegionSTRC spanLocal identityMatched residuesOTOA blocks (1-idx)
Mini-STRC700–177529.83%362distributed
ARM repeats (C-term core)1603–177033.78%148977–995, 996–1013, 1014–1067, 1068–1102, 1108–1119, 1127–1136
Peak sliding window601–65075.0%~38(local best)

ARM-repeat local identity (34%) exceeds the global average (28%) — the C-terminal ARM region is the functionally conserved paralog axis. Aligned OTOA fragments 977–1136 form a nearly contiguous 160-residue stretch (three gaps, total 12 aa missing), consistent with evolution from a common ancestor rather than opportunistic sequence matches.

Anchor residue fates (global alignment)

STRC residueWT letterOTOA equivalentConservation
K1141 (pharmacophore anion anchor)KgapSTRC-specific
G1645 (pharmacophore H-bond)GgapSTRC-specific
F1646 (pharmacophore aromatic)FF1014identical
E1659 (Misha’s mutation site)EE1027identical

The pharmacochaperone druggable pocket (Phase 2B) is partially STRC-specific — K1141 and G1645 are structural features unique to STRC. However, F1646 and E1659 are identically conserved at the equivalent OTOA positions, which is a strong cross-paralog signal for these two residues. The E1659 conservation means Misha’s mutation (E→A) disrupts a residue type that has been preserved since the STRC/OTOA divergence — reinforcing the variant’s pathogenicity assessment.

Top sliding windows (STRC → OTOA local)

STRC  601- 650: 75.0%
STRC  541- 590: 70.6%
STRC 1361-1410: 68.2%
STRC  521- 570: 66.7%
STRC  461- 510: 65.0%  (top window in prior wrong-accession run peaked here at 83%)
STRC  961-1010: 64.0%
STRC  621- 670: 63.6%
STRC 1181-1230: 63.2%
STRC  721- 770: 62.5%
STRC  361- 410: 60.9%

Peaks span both halves; multiple 60–75% identity patches distributed across STRC. OTOA is effectively a compressed paralog (1153 vs 1775 aa) carrying discontinuous fragments homologous to many STRC regions.

AAV feasibility recomputed

OTOA CDS = 1153 × 3 + 3 = 3462 bp (parent note’s 3357 bp is a different isoform estimate). With B8 enhancer (587) + polyA (250) + ITRs (290) → 4589 bp. 111 bp headroom inside 4700-bp AAV budget. Tighter than initially estimated, still feasible.

Interpretation

AvenueStatus after Phase 1A
1. Transcriptional upregulation of endogenous OTOAPlausible at sequence level (ARM paralog confirmed) — needs structural check.
2. Engineered OTOA-HTC chimeraPlausible pending structural homology — if OTOA 977–1136 superimposes on STRC 1603–1770, grafting a STRC HTC surface onto the OTOA paralog scaffold is engineering-tractable.
3. Small-molecule OTOA activatorUnchanged.

The sequence alignment alone cannot distinguish between “real functional homolog” and “evolutionary leftover with divergent fold.” The next gate is 3D superposition — see STRC OTOA Paralog Phase1B Structure Alignment.

Limitations

  • Identity alone does not predict function. Paralogs at 30% identity can have unrelated biochemistry.
  • UniProt has only signal peptide + glycosylation features — no Pfam/ZP domain calls for either protein. Structural homology inferred from external analyses.
  • Local alignment with free end gaps counts only matched residues; reported “matched” is not “total covered.”
  • The 75% peak at STRC 601–650 is in the N-terminal zone mini-STRC removes — not accessible from any mini-STRC-based design.

Replication

cd ~/STRC/models
/opt/miniconda3/bin/python3 otoa_phase1_sequence_alignment.py

Files / Models

  • ~/STRC/models/otoa_phase1_sequence_alignment.py — fetch, align, profile, anchor-map
  • ~/STRC/models/otoa_phase1_sequence_alignment.json — full metrics + features + profile

Connections

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