Supplementary Sheet S1.xlsx
A list of tools and databases used for the functional annotation based on sequences, from structures, and the construction of CAcnesDB is provided in Sheet: Tools and Databases. For each step, summary statistics are written in the adjacent sheet: summary stats. Comparison between the modeled structures from ColabFold and the available models for C. acnes in AlphaFoldDB is provided in sheet: RMSDs. The experimental structues with PDB IDs and KEGG IDs are provided in Sheet: structures PDB-CAcnesDB.

Supplementary Sheet S2.xlsx
The intermediate results for the derivation of C. acnes pocketome from the modeled structues are provided in Supplementary Sheet S2.

Supplementary Sheet S3.xlsx
The protein-ligand pairs comprising CApL and a C. acnes predicted metabolome is provided in Supplementary Sheet S3, sheets: CApL, predicted metabolome. Chemical fingerprint similarity analysis between CAcnesDB's predicted ligands and ligands reported for homologous proteins in KEGG, ChemBL and BioLiP are also provided.

Supplementary Sheet S4.xlsx
The complete list of annotation scores for all proteins with their individual evidence score is provided sheet: annotation scores. The different aspects of annotation for some given examples are also reported.

Supplementary Sheet S5.xlsx
The whole genome annotation for C. acnes KPA171202 carried out in CAcnesDB is provided in Sheet: CAcnesDB. The transporters in C. acnes (ABC transporters, transmembrane permeases and the protein export) along with their mapped ligands, are also provided.

Domains.xlsx
The predictions from InterProScan5, with the default thresholds of its member databases, were used to report PFam and InterProScan domains for the C. acnes genome. The resulting protein domains were manually checked for their association with the corresponding protein annotations.