General prediction scheme: The training sequences (S1) with known function (GOx, GOy, GOz) were searched across the protein databases, yielding hits with molecular function GO terms (GO1, GO2, GO3, GO4, GO5, GO6) and their features (see methods), sketched as dots in a two-dimensional feature space. If GO terms of the hits compared to GO terms of the query, they were classified as +1 (correct, green), and -1 otherwise (red). The classifier (SVM) separated the classes by an optimal separating hyperplane (OSH). Unknown sequences (S2) were searched in the same manner and the GO terms (GOn, GOm, GOo) were extracted. Their features were calculated and mapped into the feature space. The corresponding labels were assigned (correct/false).