An atlas of 289,962 carbohydrate-active gene clusters across the marine microbiome
mpCGCdb catalogues the carbohydrate-active enzyme gene clusters (CGCs) found in 22,607 marine genomes, with sulfatase, transporter and peptidase annotations, family phylogenies and sequence similarity networks.
Enzyme families
522 CAZyme families and subfamilies and 102 sulfatase subfamilies, each with a sequence similarity network, co-occurring families and its distribution across hosts, and 579 of them with a phylogeny.
e.g.GH16_16 β-agarase · S1_4 sulfatase
Taxonomy
Follow GTDB lineages from 136 phyla down to genus, with the clusters and enzyme families each lineage carries.
e.g. Bacteroidota › BacteroidiaGenomes and clusters
Every genome with its quality metrics and CGCs, and every CGC drawn as a gene map with its annotations.
e.g.OceanDNA-b3428 · OceanDNA-b3428_CGC1
Browse by taxonomy
How mpCGCdb was built
Genes are predicted with Pyrodigal and annotated with dbCAN (CAZymes), SulfAtlas (sulfatases), TCDB (transporters) and MEROPS (peptidases); CGCs are then mined for colocalization networks, sequence similarity networks and phylogenies. The pipeline is available as mpCGC on GitHub.
Cite mpCGCdb
If mpCGCdb informs your work, please cite:
Example pages
| Enzyme family | GH16_16 · β-agarase, β-porphyranase |
|---|---|
| Taxon | Bacteroidia · class, 61,632 CGCs |
| Genome | OceanDNA-b3428 · 26 CGCs |
| Gene cluster | OceanDNA-b3428_CGC1 |