The type III secretion system is one of the causes of a wide range of bacterial infections in human, animals and plants. This system comprises a hollow needle-like structure localized on the surface of bacterial cells that injects specific bacterial proteins, the so-called effectors, directly into the cytoplasm of a host cell. During infection, effectors convert host resources to their advantage and promote pathogenicity.
We - Tatyana Goldberg, Burkhard Rost and Yana Bromberg - at BrombergLab and RostLab developed a novel method, pEffect that predicts bacterial type III effector proteins. In our method, we combine sequence-based homology searches (through PSI-BLAST) with advanced machine learning (Profile Kernel Support Vector Machines) to accurately predict effector proteins. We use information encoded in the entire protein sequence for our predictions.