RCY1
S. cerevisiae
Rcy1p
What the model saw
Gene: RCY1 Organism: Saccharomyces cerevisiae Known functions: Rcy1p. SNARE binding. protein binding.
View unredacted entry
Rcy1p. SNARE binding. protein binding.
Solver output
RCY1 (Rcy1p) is an F-box protein in S. cerevisiae that functions in endosomal recycling by binding SNAREs (particularly Snc1p) to facilitate vesicle recycling from endosomes back to the plasma membrane and trans-Golgi network. SNARE binding is essential for proper vesicle fusion and membrane trafficking, and Rcy1p's role in recycling endosomal cargo is critical for maintaining intracellular membrane homeostasis. Defects in endosomal recycling impair autophagy flux and vacuolar/lysosomal function, which are central to proteostasis and the clearance of damaged cellular components. Loss of Rcy1p function leads to accumulation of aberrant endosomal compartments and impaired recycling, phenotypes associated with accelerated aging in yeast. Proper endosomal-to-TGN recycling also supports nutrient transporter turnover, linking Rcy1p to nutrient sensing pathways relevant to longevity.
GenAge curators classify each gene's normal function as promoting (Pro-Longevity) or opposing (Anti-Longevity) longevity, based on synthesis across studies. Loss-of-function effects can vary from this depending on the manipulation.
Advisor judgment
The model predicted RCY1 as pro_longevity, but the ground truth is anti_longevity. The model reasoned that loss of Rcy1p leads to impaired recycling and accelerated aging, which would make it pro_longevity (i.e., its presence promotes longevity). However, the GenAge database classifies it as anti_longevity, meaning RCY1 works against longevity — deletion of RCY1 likely extends lifespan. The model's mechanistic reasoning about endosomal recycling and SNARE binding is partially accurate in terms of Rcy1p's known biochemical role, but the conclusion about its effect on longevity is inverted. The model also incorrectly assigned 'disabled_macroautophagy' as the mechanism class, which is speculative and not well-supported. The confidence of 0.55 is relatively low, but the model still committed to the wrong direction. The reasoning quality is poor because it incorrectly inferred the direction of longevity influence from the gene's function.
Raw API responses
solver
{
"reasoning": "RCY1 (Rcy1p) is an F-box protein in S. cerevisiae that functions in endosomal recycling by binding SNAREs (particularly Snc1p) to facilitate vesicle recycling from endosomes back to the plasma membrane and trans-Golgi network. SNARE binding is essential for proper vesicle fusion and membrane trafficking, and Rcy1p's role in recycling endosomal cargo is critical for maintaining intracellular membrane homeostasis. Defects in endosomal recycling impair autophagy flux and vacuolar/lysosomal function, which are central to proteostasis and the clearance of damaged cellular components. Loss of Rcy1p function leads to accumulation of aberrant endosomal compartments and impaired recycling, phenotypes associated with accelerated aging in yeast. Proper endosomal-to-TGN recycling also supports nutrient transporter turnover, linking Rcy1p to nutrient sensing pathways relevant to longevity.",
"confidence": 0.55,
"key_pathways": [
"endosomal recycling / SNARE-mediated vesicle fusion",
"vacuolar/lysosomal trafficking and autophagy",
"nutrient transporter recycling"
],
"mechanism_class": "disabled_macroautophagy",
"longevity_influence": "pro_longevity"
}advisor
{
"notes": "The model predicted RCY1 as pro_longevity, but the ground truth is anti_longevity. The model reasoned that loss of Rcy1p leads to impaired recycling and accelerated aging, which would make it pro_longevity (i.e., its presence promotes longevity). However, the GenAge database classifies it as anti_longevity, meaning RCY1 works against longevity — deletion of RCY1 likely extends lifespan. The model's mechanistic reasoning about endosomal recycling and SNARE binding is partially accurate in terms of Rcy1p's known biochemical role, but the conclusion about its effect on longevity is inverted. The model also incorrectly assigned 'disabled_macroautophagy' as the mechanism class, which is speculative and not well-supported. The confidence of 0.55 is relatively low, but the model still committed to the wrong direction. The reasoning quality is poor because it incorrectly inferred the direction of longevity influence from the gene's function.",
"failure_mode": "confident_wrong",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 2,
"ground_truth_questionable": false
}