Ad-Hoc Bioinformatics Analysis Project

Warnings (1)

Ad-Hoc Bioinformatics Analysis Project

Overview

This project tracks cases where AI-assisted gene review required computational analysis beyond standard database lookups to validate or refute annotations. These analyses demonstrate the value of integrating bioinformatics capabilities into the curation workflow.

The agentic AI system can:
- Write and execute Python code for sequence analysis
- Query structural databases (PDB, AlphaFold)
- Perform domain architecture analysis
- Compare sequences across species
- Validate active site residues

Source: Presented at Gene Ontology Consortium Meeting, October 2025, Cambridge UK. See ai4curation/ai-gene-review.

Categories of Bioinformatics Analysis

1. Active Site Validation

Purpose: Verify whether proteins with enzyme-like domains have conserved catalytic residues.

Example - Epe1 (S. pombe):
- JmjC domain suggests histone demethylase activity
- Analysis revealed: HVD instead of canonical HXD motif
- Missing Fe(II)-binding histidine residues
- Conclusion: Pseudo-enzyme lacking catalytic activity
- Location: genes/pombe/[Epe1](../../genes/SCHPO/Epe1/Epe1-ai-review.html)/Epe1-bioinformatics/

2. Domain Architecture Analysis

Purpose: Map protein domains and compare to characterized homologs.

Example - AcrF8 (phage ZF40):
- Small 92-residue protein
- Analysis of protein-protein and protein-RNA interaction surfaces
- Structural comparison to other Type I-F anti-CRISPRs
- Conclusion: Unique dual-binding mechanism

3. Substrate Specificity Prediction

Purpose: Determine whether predicted enzymatic activity matches actual substrate.

Example - PHYKPL (human):
- Classified in aminotransferase III family
- Sequence analysis showed it functions as phospho-lyase
- Active site comparison to characterized family members
- Conclusion: Not a transaminase despite domain classification

4. Cofactor Binding Site Analysis

Purpose: Validate cofactor binding predictions.

Example - Epe1 JmjC domain:
- Fe(II) binding predicted from domain
- Analysis of metal coordination residues
- Comparison to active JmjC demethylases
- Conclusion: Cannot coordinate Fe(II) due to substitutions

5. Localization Signal Prediction

Purpose: Validate predicted localization based on signal sequences.

Example - LPL1 (C. albicans):
- Predicted transmembrane domain (residues 286-306)
- Analysis suggests hydrophobic region for lipid droplet association
- Conclusion: Not a membrane protein; lipid droplet localized

Genes with Bioinformatics Analyses

Gene Species Analysis Type Key Finding Status
Epe1 pombe Active site, cofactor binding Pseudo-demethylase, no Fe(II) binding COMPLETE
AcrF8 BPZF4 Domain architecture, structure Dual protein-RNA binding mechanism COMPLETE
PHYKPL human Substrate specificity Phospho-lyase, not transaminase COMPLETE
LPL1 CANAL Localization signals Lipid droplet, not membrane COMPLETE

Analysis Resources

Bioinformatics Folders

Each gene with computational analysis has a dedicated folder:

genes/<species>/<gene>/<gene>-bioinformatics/
├── RESULTS.md           # Summary of findings
├── *.py                 # Analysis scripts
├── data/                # Input data
└── results/             # Output files

Common Tools Used

Best Practices

  1. Reproducibility: All analyses should be scripted, not manual
  2. Documentation: RESULTS.md summarizes key findings
  3. Citations: Reference bioinformatics results in annotations
  4. Limitations: Acknowledge when analysis is inconclusive

When to Perform Bioinformatics Analysis

Consider computational analysis when:
- Domain-based predictions conflict with literature
- Active site conservation is questioned
- Substrate specificity is ambiguous
- Localization predictions seem inconsistent
- Pseudo-enzyme status is suspected

STATUS

Completed Analyses

Bioinformatics Folders

Last updated: 2026-01-22

NOTES

2026-01-22

Project Creation

Documented cases where ad-hoc bioinformatics resolved annotation ambiguities.

Key Insight: The most valuable bioinformatics application is active site validation for enzymes. Many proteins are annotated with enzymatic activity based on domain presence (IEA), but lack conserved catalytic residues.

Epe1 Example:
- JmjC domain → 7 enzymatic activity annotations
- Active site analysis → HVD instead of HXD, no Fe(II) binding
- Result: All 7 enzymatic annotations marked REMOVE

This demonstrates how computational analysis can systematically identify pseudo-enzymes and prevent annotation errors from propagating.