Hi,

You can use the SMURF (Secondary Metabolites Unique Region Finder) tool from J. Craig Venter Institute. It identifies PKS genes from user provided protein sequences in FASTA format, and predicts which genes are part of the biosynthetic cluster based on genome coordinate information.

Yet another method you can try for bacteria with a python based software called Dynamite which can be used to identify natural product bio synthetic gene clusters encoded in nucleotide/protein sequences within in the entire NCBI databank.This shows gene clusters of PKS 1,PKS 2 ,PKS 3 etc based on hits and GI- GeneInfo Identifier number range.

The Gene clusters displaying bio synthetic characteristics of interest can also be manually downloaded as .gb file format( DNA encoding file format) from NCBI, guided by Dynamite summary files, and are subjected to further manual analysis using standard software such as Vector NTI.

All the best...