data/gene_unknown/README.md

JCVI Syn3.0 Unknown Genes

This directory contains protein sequences from the JCVI Syn3.0 minimal bacterial genome that were annotated as "unknown function" or "generic".

Source

JCVI Syn3.0 is the minimal bacterial genome created by the J. Craig Venter Institute:

Hutchison CA 3rd, et al. "Design and synthesis of a minimal bacterial genome." Science. 2016 Mar 25;351(6280):aad6253. DOI: 10.1126/science.aad6253

The 473-gene genome was systematically reduced from Mycoplasma mycoides to identify the minimal set of genes required for life.

Files

File	Description
unknown_aa_seqs.fasta	149 protein sequences with unknown/generic function
unknown_aa_seqs.npy	Pre-computed Protein-Vec embeddings (149 × 512)

Gene Naming

• MMSYN1_XXXX - Gene identifier in Syn3.0
• 1=Unknown - Gene with unknown function
• 2=Generic - Gene with generic/broad annotation

Results

Using conformal protein retrieval at 10% FDR (α=0.1):

• 59/149 (39.6%) of unknown genes can be confidently annotated
• Results reproduced in notebooks/pfam/genes_unknown.ipynb
• See paper Figure 2A for visualization

Citation

If using this data, please cite both the CPR paper and the original Syn3.0 paper:

@article{boger2025conformal,
  title={Functional protein mining with conformal guarantees},
  author={Boger, Ron S and Chithrananda, Seyone and Angelopoulos, Anastasios N and Yoon, Peter H and Jordan, Michael I and Doudna, Jennifer A},
  journal={Nature Communications},
  volume={16},
  pages={85},
  year={2025},
  doi={10.1038/s41467-024-55676-y}
}

@article{hutchison2016design,
  title={Design and synthesis of a minimal bacterial genome},
  author={Hutchison, Clyde A and Chuang, Ray-Yuan and Noskov, Vladimir N and others},
  journal={Science},
  volume={351},
  number={6280},
  pages={aad6253},
  year={2016},
  doi={10.1126/science.aad6253}
}