Fungi-Kcr: A Language Model for Predicting Lysine Crotonylation in Pathogenic Fungal Proteins

Yong-Zi Chen^1*Fengxiao Wang²Zhuo-Zhi Wang³Haixin Li^1*

• ¹Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
• ²Shanxi Normal University, Linfen, Shanxi Province, China
• ³Tianjin Medical University, Tianjin, Tianjin Municipality, China

Lysine crotonylation (Kcr) is an important post-translational modification (PTM) of proteins, playing a key role in regulating various biological processes in pathogenic fungi.However, the experimental identification of Kcr sites remains challenging due to the high cost and time-consuming nature of mass spectrometry-based techniques. To address this limitation, we developed Fungi-Kcr, a deep learning-based model designed to predict Kcr modification sites in fungal proteins. The model integrates convolutional neural networks (CNN), gated recurrent units (GRU), and word embedding to effectively capture both local and long-range sequence dependencies. Comprehensive evaluations, including ten-fold cross-validation and independent testing, demonstrate that Fungi-Kcr achieves superior predictive performance compared to conventional machine learning models. Moreover, our results indicate that a general predictive model performs better than species-specific models. These findings suggest that despite species-specific variations, certain residues near Kcr sites show consistent enrichment or depletion patterns, implying potential shared regulatory features or substrate preferences among the pathogenic fungi studied. The proposed model provides a valuable computational tool for the large-scale identification of Kcr sites, contributing to a deeper understanding of fungal pathogenesis and potential therapeutic targets. The source code and dataset for Fungi-Kcr are available at https://github.com/zayra77/Fungi-Kcr.