Abstract
Secretory effectors from pathogenic microorganisms significantly influence pathogen survival and pathogenicity by manipulating host signalling, immune responses, and metabolic processes. However, because of sequence and structural heterogeneity among bacterial effectors, accurately classifying multiple types simultaneously remains challenging. Therefore, we developed TXSelect, a multi-task learning framework that simultaneously classifies TXSE (types I, II, III, IV and VI secretory effectors) using a shared backbone network with task-specific heads. TXSelect integrates the protein embedding features of evolutionary scale modelling (ESM), particularly the N-terminal mean, with classical descriptors to effectively capture complementary information. These descriptors include distance-based residue (DR) and split amino acid composition general (SC-PseAAC-General). Rigorous evaluation identified ESM N-terminal mean + DR + SC-PseAAC as the optimal feature combination, achieving high accuracy (validation F1 = 0.867, test F1 = 0.8645) and robust generalization. Comprehensive assessments and visualization with Uniform Manifold Approximation and Projection further validated the discriminative capability and interpretability of the model. TXSelect provides an efficient computational tool for accurately classifying bacterial effectors, supporting deeper biological understanding and potential therapeutic development.