SBSPKS is a webserver for carrying out sequence and structure based analysis of Polyketide Synthases, an important family of multifunctional megasynthases involved in the biosynthesis of a variety of pharmaceutically important secondary metabolites. The knowledge base for development of SBSPKS is derived from a comprehensive bioinformatics analysis of the sequence and structural features of a large number of experimentally characterized PKS gene clusters having known metabolic products and recently available crystal structures of PKS and FAS proteins.
The interfaces for carrying out various tasks by SBSPKS are organized as three major functional units, namely NRPS_PKS, Model_3D_PKS and Dock_Dom_Anal .
Model_3D_PKS can be used for modeling the biologically active dimeric structures for complete PKS modules using available crystal structures of PKS and FAS proteins as structural templates. It also provides interfaces for visualizing the relative orientation of various catalytic domains and structured linker regions within the module and identify crucial residues involved in inter domain interactions.
Dock_Dom_Anal identifies the key interacting residue pairs in inter subunit interfaces based on alignment of terminal inter polypeptide linkers on the docking domain structure. In case of modular PKS with multiple ORFs, it combinatorially evaluates all possible interface contacts and ranks each ORF combination in terms of number of favorable interface contacts. This analysis can thus help in predicting the order of substrate channeling in a modular PKS clusters.
NRPS-PKS is the updated version of the web servers developed earlier by our group for sequence based analysis of PKS/NRPS proteins. It provides a number of user friendly tools for sequence based analysis of putative PKS/NRPS proteins.
In summary, SBSPKS is a valuable resource for predicting biosynthetic products of uncharacterized PKS clusters and rational design of engineered polyketides.
CITING SBSPKS and related Webservers :
1) Anand, S., Prasad, M.V.R., Yadav, G., Kumar, N., Shehara, J., Ansari, M.Z. and Mohanty, D. (2010) SBSPKS: Structure based sequence analysis of polyketide synthases. Nucleic Acids Res, 38, W487-96. PUBMED
2) Yadav, G., Gokhale, R.S. and Mohanty, D. (2009) Towards prediction of metabolic products of polyketide synthases:an insilico analysis. PLoS Comput Biol, 5, e1000351. PUBMED
3) Ansari, M.Z., Yadav, G., Gokhale, R.S. and Mohanty, D. (2004) NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases. Nucleic Acids Res, 32, W405-413. PUBMED
4) Yadav, G., Gokhale, R.S. and Mohanty, D. (2003) SEARCHPKS: A program for detection and analysis of polyketide synthasedomains. Nucleic Acids Res , 31,3654-8. PUBMED
5) Yadav, G., Gokhale, R.S. and Mohanty, D. (2003) Computational approach for prediction of domain organization and substrate specificity of modular polyketide synthases. J Mol Biol, 328, 335-363. PUBMED