An iterative method is developed to generalize the original pathway model which identifies not simply the strongest pathway involved in the protein-mediation of electron transfer matrix elements but all the relevant ones. The generalized pathway model is a semianalytical, nonperturbative, and computationally tractable method that allows detail investigation of the electron tunneling propagation in the protein medium for any one-electron Hamiltonian, and to examine structure-function relationships in multiple pathway regimes that may be induced by hydrogen bond and through-space contacts in the folded protein structure. This method enables an understanding of how details of the 3-D protein structures control the tunneling process, and whether pathway interference in the protein structural motifs causes substantial deviation from standard pathway analysis.