BGC Classes
How clusters are classified by their biosynthetic machinery
A BGC class describes the type of enzymatic logic a cluster uses to assemble its product — the assembly line, not the molecule that comes off it. (For the molecule, see the predicted ChemOnt chemistry.) The class is a normalised label derived from the protein domains detected in the cluster, so it reflects the genetics, not a chemical assay.
The class appears as the Class column in the roster, a chip in the iBGC detail, and the BGC class filter.
Why class and chemistry differ
A Polyketide cluster uses polyketide synthase (PKS) enzymes to extend a carbon chain. The product might be a macrolide, an aromatic polyketide, or a linear polyketide — different molecules, same machinery. The class tells you about the assembly line; the ChemOnt annotation tells you about the product.
The major classes
Polyketide (PKS)
Logic: Polyketide synthases — modular enzymes that extend a carbon chain by iteratively adding two-carbon units, with optional reduction, dehydration, or methylation per module.
| Subclass | Description | Examples |
|---|---|---|
| Macrolide | Large macrolactone ring, formed by a cyclising thioesterase. | Erythromycin, pikromycin |
| Aromatic | Aromatic rings built by iterative (type II) PKS. | Tetracycline, doxorubicin |
| Linear | Linear or minimally cyclised chains. | Mupirocin |
Non-ribosomal peptide (NRPS)
Logic: Non-ribosomal peptide synthetases — modular enzymes that select, activate, and join amino acids (including non-proteinogenic ones) without the ribosome.
| Subclass | Description | Examples |
|---|---|---|
| Cyclic | Cyclised peptides, often with cross-links, D-amino acids, or N-methylation. | Vancomycin, daptomycin |
| Linear | Linear peptides or lipopeptides. | Gramicidin, surfactin |
RiPP
Logic: Ribosomally synthesised precursor peptides extensively modified by tailoring enzymes in the same cluster (cyclisation, dehydration, thioether bridges, …).
| Subclass | Description | Examples |
|---|---|---|
| Lanthipeptide | Lanthionine thioether bridges. | Nisin, mersacidin |
| Thiopeptide | N-containing heterocycle plus thiazole/oxazole rings. | Thiostrepton |
| Sactipeptide | Sulfur-to-α-carbon thioether bonds (radical SAM). | Subtilosin A |
Terpene
Logic: Terpene synthases/cyclases convert linear prenyl diphosphate precursors into cyclic terpene scaffolds via carbocation cascades.
| Subclass | Description | Examples |
|---|---|---|
| Sesquiterpene | Three isoprene units (C15). | Pentalenene |
| Diterpene | Four isoprene units (C20). | Gibberellin |
Saccharide
Logic: Glycosyltransferases and sugar-modifying enzymes building specialised sugar or aminosugar products, often in concert with other classes.
| Subclass | Description | Examples |
|---|---|---|
| Aminoglycoside | Aminosugar antibiotics. | Streptomycin, kanamycin |
Alkaloid
Logic: Diverse routes producing nitrogen-containing heterocycles; individual enzymes catalyse specific transformations on amino-acid-derived precursors (not modular assembly lines).
| Subclass | Description | Examples |
|---|---|---|
| Indole | Indole ring, usually from tryptophan. | Staurosporine |
| Pyrrolidine | Pyrrolidine ring, from proline/ornithine. | Prodiginine-related |
Other
Clusters using legitimate but less common strategies that don’t fit the major classes — for example phosphonates (C–P bond; fosfomycin) and aminocoumarins (novobiocin). “Other” is not a low-quality label; some of the most interesting discoveries sit here.
Hybrid clusters
Some clusters encode enzymes from more than one class (for example a PKS–NRPS hybrid). The platform labels these as a hybrid class. When you filter by a class, a hybrid that includes it matches.
Filtering by class
The BGC class filter lets you pick a broad class or a subclass; selecting a broad class includes its subclasses. Combine it with the ChemOnt filter when you want a specific product chemistry within a class (e.g. polyketide clusters predicted to make macrolides).
Tips
- Class reflects the enzyme, not the product; use ChemOnt to filter by predicted chemistry.
- Hybrids are common in actinobacteria — expect many when exploring Streptomyces.
- Confirm a class by clicking into the cluster’s genes in the protein panel to read its domain architecture directly.