0.HRGMv2_Proteins/
: All protein sequences predicted from all genomes, unique protein sequences after redundancy removal, and five classes of protein catalogs clustered at different identity thresholds (100%, 95%, 90%, 70%, 50%)
    - 0.Redundant_CDS/ : All redundant CDS sequences (549,278,140 coding sequences from 230,632 redundant NC genomes)     - 1.HRGMv2_Unique_Proteins/ : Unique protein sequences after redundancy removal     - 2~6.HRGMv2_{identity}_Proteins/ : Clustered protein catalogs at 100%, 95%, 90%, 70%, and 50% identity thresholds 1.HRGMv2_Pangenomes/
: RGI and eggNOG-mapper results for 4,824 HRGMv2 species (predicted from species-specific pangenomes)
    - emapper_results/ : Output of eggNOG-mapper     - rgi_results/ : Output of RGI (Resistance Gene Identifier) 2.HRGMv2_CAZymes/
: Output of run_dbcan v4.1.4 (standalone version of dbCAN3). CAZyme families were annotated from 155,211 non-redundant genomes.     - For bulk download: download_link_info_cazyme.tsv (full download paths for each non-redundant genome) 3.HRGMv2_Defense_systems/
: Output of DefenseFinder for genome-resolved detection of bacterial defense systems.     - For bulk download: 3.HRGMv2_Defense_systems.tar.gz (archive of the full folder) * Folder structure for 2.HRGMv2_CAZymes/ and 3.HRGMv2_Defense_systems/ follows a 4-level hierarchy to facilitate navigation:

2.HRGMv2_CAZymes/ or 3.HRGMv2_Defense_systems/  ← Root
└── HRGMv2_20XX/                                ← Level 1 (group of 100s)
    └── HRGMv2_204X/                            ← Level 2 (group of 10s)
        └── HRGMv2_2040/                        ← Level 3 (species-level folder)
            ├── GENOME008241.tar.gz            ← Level 4 (result archive)
            └── ...