Metabolic networks are represented by the set of metabolic pathways. Metabolic pathways are a series of chemical reactions, in which the product from one reaction serves as the input to another reaction. Many pathways remain incompletely characterized, and in some of them not all enzyme components have been identified. One of the major challenges of computational biology is to obtain better models of metabolic pathways. Existing models are dependent on the annotation of the genes. This propagates error accumulation when the pathways are predicted by incorrectly annotated genes. Pairwise kernel frameworks have been used in supervised learning approaches, e.g., Pairwise Support Vector Machines (SVMs), to predict relationships among two pairs of entities. Rational kernels are based on transducers to manipulate sequence data, computing similarity measures between sequences or automata. Rational kernels take advantage of the smaller and faster representation and algorithms of weighted finite-state transducers. They have been effectively used in problems that handle large amount of sequence information such as protein essentiality, natural language processing and machine translations. We propose a new framework, Pairwise Rational Kernels (PRKs), to manipulate pairs of sequence data, as pairwise combinations of rational kernels. We develop experiments using SVM with PRKs applied to metabolic pathway predictions in order to validate our methods. As a result, we obtain faster execution times with PRKs than other kernels, while maintaining accurate predictions. Because raw sequence data can be used, the predictor model avoids the errors introduced by incorrect gene annotations. We also obtain a new type of Pairwise Rational Kernels based on automaton and transducer operations. In this case, we define new operations over two pairs of automata to obtain new rational kernels. We also develop experiments to validate these new PRKs to predict metabolic networks. As a result, we obtain the best execution times when we compare them with other kernels and the previous PRKs.