Remote homology detection is among the most intensively researched problems in bioinformatics. Currently discriminative approaches, especially kernel-based methods, provide the most accurate results. However, kernel methods also show several drawbacks: in many cases prediction of new sequences is computationally expensive, often kernels lack an interpretable model for analysis of characteristic sequence features, and finally most approaches make use of so-called hyperparameters which complicate the application of methods across different datasets.