NRPS/PKS substrate predictor
This application is aimed at predicting the substrate specificity of Adenylation (A)-domains of NRPSs and Acetyl Transferase (AT)-domains of PKSs and has been created to support:
Khayatt BI, Overmars L, Siezen RJ and Francke C, Classification of the adenylation and acyl-transferase activity of NRPS and PKS systems using ensembles of substrate-specific Hidden Markov Models.
A FASTA file containing the domain sequence(s) can be used as input and after selecting the appropriate domain-type the prediction can be started by "submit".*
The output will be given in tab-delimited format and provides a substrate prediction based on the Hidden Markov Models created by us (www.cmbi.ru.nl/NRPS-PKS-substrate-predictor/; please cite: Khayatt et al.). N/A will be returned in case no reliable prediction can be made.
* Remark: To ensure a proper prediction it is essential to use only the sequence of the A or AT domain from the complete NRPS or PKS sequence, respectively. To identify and extract the domain boundaries from the protein sequence of the complete system we advise to use the search domain option in either of these tools
- NRPS-PKS tool (please cite: Ansari et al. Nucleic Acids Res 2004, 32:W405-413)
- PKS/NRPS analysis tool (please cite: Bachmann and Ravel, Methods Enzymol. 2009, 458:181-217)
- ASMPKS (please cite Tae et al., BMC Bioinformatics 2007, 8:327)
- antiSMASH 2.0 (please cite Medema et al., Nucleic Acids Res 2011, 39, W339-W346)