GprotPRED

GprotPRED classifies heterotrimeric G-protein subunits from protein sequences, assigning Gα subunits to the Gs, Gi/o, Gq/11, and G12/13 families and identifying Gβ and Gγ.

Key Features:

• pHMM set: Six specific profile Hidden Markov Models (pHMMs) are used to identify and classify Gα (Gs, Gi/o, Gq/11, G12/13), Gβ, and Gγ subunits from protein sequences.
• Target coverage: Models explicitly cover all three heterotrimeric G-protein subunits (Gα, Gβ, Gγ) and the four Gα families.
• Input type: Operates on protein sequence data.
• Validation and performance: For all pHMMs except Gβ, sensitivity and specificity are reported as 100%; the Gβ model has sensitivity 100% and specificity 99.993%.
• Family-level classification: Provides family assignment for Gα subunits rather than just generic Gα detection.
• Proteome-scale detection: Demonstrated ability to identify all known G-protein subunits across ten proteomes and to detect novel proteins in 27 arthropod proteomes.

Scientific Applications:

• Proteome annotation: Annotation and classification of heterotrimeric G-protein subunits in whole proteomes.
• Re-annotation of uncertain proteins: Providing more credible classifications for proteins with uncertain or imprecise annotations.
• Novel subunit discovery: Detection of previously unannotated G-protein subunits in arthropod proteomes.
• Comparative annotation: Enabling family-level differentiation of Gα subunits for comparative genomics and functional inference.

Methodology:

Six profile Hidden Markov Models (pHMMs) were constructed and validated to detect and classify Gα (Gs, Gi/o, Gq/11, G12/13), Gβ, and Gγ subunits from protein sequences.