Hello parijat, as far as matabolic pathway is concerned, you can use either Cell designer and/or Simbiolgy to create your matabolic pathways, I have been using these tools for Signal transduction cascade modeling.
If you had information of protein names and the organism to which those protein belongs to, then KEGG is he best server for annotating metabolic pathway. If you tell us the organism name, I will search for the specific link.