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)
            └── ...