Prediction and reconstruction of metabolic pathways from rudimentary molecular data is a fundamental way to understand the logic of life. Comparing metabolic pathways are important to identify conservation and variations among different biology systems. Alignment is a strong indicator of the biologically significant relationship. In this article, a definition of metabolic pathway is presented. An alignment algorithm and a computational system are developed to reveal the similarities between metabolic pathways. A web-based program for prediction and alignment of metabolic pathway, PathAligner, is available at http://bibiserv.techfak.uni-bielefeld.de/pathaligner.