Secondary metabolism (also called specialized metabolism) refers to pathways and small molecule products of metabolism that are not absolutely required for the survival of the organism. Secondary metabolites are produced by many microbes, plants, fungi and animals. Bacterial secondary metabolites are an important source of antimicrobial and cytostatic drugs. These molecules are often synthesized in a stepwise fashion by multimodular megaenzymes that are encoded in clusters of genes encoding enzymes for precursor supply and modification.
Antismash is a tool predicting secondary metabolite gene clusters in bacterial genomes.
Know more <mage_antiSMASH>
about antiSMASH.
These result are linked to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) database.
Secondary metabolites gene clusters predictions are available through the Metabolism section and the Secondary Metabolites subsection, in the main navigation menu.
This table enumerates all secondary metabolite regions predicted for the selected organism and its replicons.
- Region id: Identifier of the region. Click on it to open the detailled
antiSMASH cluster visualization window <domainviewer>
page, which allows you to visualize the full antiSMASH cluster prediction and its genomic context. - Replicon name and Replicon type give characteristics of the replicon where the region is found.
- Begin, End and Length give informations about the location and the length of the region on the sequence.
- Region type: Type of the region, predicted by antiSMASH.
- MIBiG: MIBiG region identifier with the best hit (if any), click on it to open the MIBiG website page related to this MIBiG.
- Completion: Completion of the best hit between MIBiG region and antiSMASH predicted region (if any hit). See below for more information about its computation.
- Product and Type: Product and type of the MIBiG compound.
The completion is computed as follow :
Where:
- nb_of_hit = number of genes with blast hit in the antiSMASH predicted region and MIBiG region
- nb_of_mibig_gene = number of all genes in the MIBiG curated region
This means that when 2 or more genes in a single MIBiG curated region are similar, the same gene in pkgdb can hit on these MIBiG gene. When this happen, the completion can be higher than 1 (represented by 1*).