mpCGCdb mpCGCdbMarine polysaccharide CAZyme gene clusterer database
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Downloads 21 bulk tables · 1.6 GB total · CC-BY 4.0

Bulk tables hosted on Zenodo

All tables below are mirrored to a citable Zenodo record with a permanent DOI.

Record: https://zenodo.org/records/20219287

Each download link goes straight to the file on Zenodo.

Primary tables 4 files

all_cgc_magmapped.tsv
All CGC genes
350.1 MB
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One row for each gene in every CGC, with the CGC number, genome, gene type, contig, protein ID, coordinates, strand and annotation.
mag_metadata.txt
Genome metadata
5.1 MB
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Completeness, contamination, GC content, N50, gene count and GTDB lineage for each genome, along with Cas, MGE, WD40 and ARG annotations.
mag_taxonomy.tsv
Genome taxonomy groups
851 KB
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The broad taxonomic group used on the site (for example Gammaproteobacteria, Bacteroidota or Archaea) for each genome, listed by bin ID. Full GTDB r207 lineages are in mag_metadata.txt.
gomc_metadata.tsv
GOMC genome metadata
5.7 MB
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The genome table as distributed by GOMC: the same quality metrics and GTDB r207 lineage as mag_metadata.txt, plus each bin's original name and source label.

Sequence clustering / SSN 8 files

global_clusters_r1p0.tsv
Leiden communities (r = 1.0)
123.9 MB
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The community each protein belongs to at resolution 1.0. This is the partition used across the site.
global_clusters_r0p5.tsv
Leiden communities (r = 0.5)
123.8 MB
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The partition at resolution 0.5: 67,527 communities, against 67,685 at r = 1.0.
global_clusters_r4p0.tsv
Leiden communities (r = 4.0)
124.1 MB
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The partition at resolution 4.0: 68,058 communities, against 67,685 at r = 1.0.
global_protein_to_cgc.tsv
Protein to CGC map
179.1 MB
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The CGC that each of the 2.44 million proteins belongs to.
global_protein_annotation.tsv
Protein annotations
125.2 MB
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One label per protein: its top CAZyme or sulfatase subfamily, or its transporter, peptidase, regulator or signal-transduction class, from the dbCAN HMMER, DIAMOND and dbCAN-sub searches.
global_protein_category.tsv
Protein categories
129.8 MB
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A broad category for each protein: CAZyme, sulfatase, transporter, peptidase, regulator or other.
global_scone_edges.tsv
Similarity-colocalization network (SCoNe) edges
22.6 MB
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Co-occurrence weights between pairs of communities. These are the edges of the SCoNe network.
global_scone_layout.tsv
SCoNe layout coordinates
4.4 MB
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2D coordinates of the SCoNe network nodes, matching the Cytoscape sessions.

Community-level summaries 2 files

global_community_reps.tsv
Community representatives
2.8 MB
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The representative protein, top family call, member count and host distribution of each community.
global_community_interpro.tsv
InterPro architectures per community
6.1 MB
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The InterPro domain architectures found in each community, including the most common one.

Annotation references 4 files

cazy_metadata.tsv
CAZy family metadata
78 KB
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Activities, EC numbers and substrates from CAZy for each GH, PL, CE, AA, GT and CBM family.
sulfatlas_metadata.tsv
SulfAtlas family metadata
372 B
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Subfamily summaries from SulfAtlas v2.4 (S1, S2 and S3).
sulfatlas_curated.tsv
SulfAtlas EC numbers and activities
3 KB
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EC numbers and substrates for sulfatase subfamilies with characterised members, from SulfAtlas.
ec_functions.tsv
EC number functions
609 KB
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EC numbers and their reactions, from the ENZYME database (ENZYME.DAT).

Representatives & FASTAs 3 files

representatives.tsv
Representative proteins
420.1 MB
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The representative protein of each community and where to find it in the FASTA files.
noncatalytic_cgcs.tsv
Non-catalytic CGCs
4.7 MB
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CGCs whose only CAZyme hits are to non-catalytic families, such as CBMs.
gomc_nmpfs.tsv
Novel metagenomic protein families (NMPFs)
1.6 MB
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Novel protein families identified from the sequence similarity network.

Per-family and per-genome files

Each family and genome page has its own data files. To download many at once, point wget or curl at the matching folder:

Per family https://mpcgcdb.com/<family>/{cgcs.txt, ranked_families.tsv}, for example GH13/cgcs.txt
Per genome https://mpcgcdb.com/genomes/<bin_id>/{cgcs.txt, proteins.tsv, ranked_families.tsv}

Protein sequences are not provided per family or genome. The full protein catalog can be downloaded from the Global Ocean Microbiome Catalog.

File names stay the same between releases. The code for the pipeline is on GitHub.

License & reuse

All tables on this page are released under CC BY 4.0. You are free to reuse them with attribution. Please cite mpCGCdb along with the original sources (CAZy, SulfAtlas, GTDB, GOMC) where they apply. The recommended citation is on the About page.