The secondary metabolite gene cluster prediction tool antiSMASH has been updated to version 3 on the MicroScope platform. This new version includes updated and extended cluster identification profiles, especially for ribosomally synthesised peptide products (RiPPs) [1]. Moreover predicted clusters are compared to the recently published reference database MIBiG (Minimal Information about a Biosynthetic Gene cluster), which aims at developing a genomic standard for experimentally characterized biosynthetic gene clusters (BGC) of all types (NRPS, PKS or RIPP) and from all phyla (bacteria, fungi or plants)[2]. This database provides a comprehensive and standardized specification for BGC annotations and gene cluster-associated metadata.
You can now get a complete view of secondary metabolite gene cluster prediction for one organism by using the Antismash section of the Metabolism menu.
The cluster visualization window has been improved with new graphical representations and chemical structure predictions. For NRPS/PKS cluster type, the predicted peptide monomer composition and its corresponding the SMILE formula are specified. The chemical structure prediction visualization is displayed as well.
Below the graphical representation of the predicted antiSMASH cluster, you find 3 tables:
- The MIGiB Clusters Similarities table provides information about similar known clusters described in MIBiG database.
- The Genomic Objects table provides informations regarding the genomic objects depicted in the graphical representation.
- The Tailoring Clusters Similarities table provides informations about genes which may be involved in tailoring reactions already described in other BGCs.
Additional functionalities will be added in the near future. Stay tuned on the MicroScope platform !
References:
[1] Weber T, et al. (2015) antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 2015 Jul 1;43(W1):W237-43.
[2] Medema MH, et al. (2015) Minimum Information about a Biosynthetic Gene cluster. Nat Chem Biol. 2015 Sep;11(9):625-31.