AMD1
S. cerevisiae
AMP deaminase
What the model saw
Gene: AMD1 Organism: Saccharomyces cerevisiae Known functions: AMP deaminase. AMP deaminase activity. deaminase activity. protein binding. zinc ion binding.
View unredacted entry
AMP deaminase. AMP deaminase activity. deaminase activity. protein binding. zinc ion binding.
Solver output
AMD1 encodes AMP deaminase, which catalyzes the irreversible deamination of AMP to IMP, thereby reducing cellular AMP levels. AMP is a critical activator of AMPK (Snf1 in yeast), the master energy-sensing kinase that promotes longevity through inhibition of TORC1 and activation of autophagy and stress responses. By depleting AMP, AMD1 activity suppresses Snf1/AMPK signaling, effectively mimicking a nutrient-replete state and dampening pro-longevity energy-sensing pathways. Elevated AMP deaminase activity would thus shift the AMP:ATP ratio downward, reducing the cell's ability to sense low-energy states and engage lifespan-extending metabolic programs. Loss of AMD1 function, conversely, would raise AMP levels and enhance Snf1 activation, consistent with a pro-longevity outcome.
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 correctly predicted AMD1 as anti_longevity. The mechanistic reasoning is plausible and well-constructed: AMD1 (AMP deaminase) converts AMP to IMP, reducing AMP levels, which would suppress Snf1/AMPK activation and thus dampen pro-longevity energy sensing pathways. This is a reasonable mechanistic explanation for why AMD1 deletion would extend lifespan. The reasoning is coherent and biologically sound, though it's somewhat speculative in connecting all the dots (the actual experimental evidence may involve different mechanisms). The confidence level of 0.62 is appropriately calibrated. Overall a strong prediction with good mechanistic reasoning.
Raw API responses
solver
{
"reasoning": "AMD1 encodes AMP deaminase, which catalyzes the irreversible deamination of AMP to IMP, thereby reducing cellular AMP levels. AMP is a critical activator of AMPK (Snf1 in yeast), the master energy-sensing kinase that promotes longevity through inhibition of TORC1 and activation of autophagy and stress responses. By depleting AMP, AMD1 activity suppresses Snf1/AMPK signaling, effectively mimicking a nutrient-replete state and dampening pro-longevity energy-sensing pathways. Elevated AMP deaminase activity would thus shift the AMP:ATP ratio downward, reducing the cell's ability to sense low-energy states and engage lifespan-extending metabolic programs. Loss of AMD1 function, conversely, would raise AMP levels and enhance Snf1 activation, consistent with a pro-longevity outcome.",
"confidence": 0.62,
"key_pathways": [
"AMPK/Snf1 energy sensing",
"AMP/ATP ratio regulation",
"TORC1 signaling"
],
"mechanism_class": "deregulated_nutrient_sensing",
"longevity_influence": "anti_longevity"
}advisor
{
"notes": "The model correctly predicted AMD1 as anti_longevity. The mechanistic reasoning is plausible and well-constructed: AMD1 (AMP deaminase) converts AMP to IMP, reducing AMP levels, which would suppress Snf1/AMPK activation and thus dampen pro-longevity energy sensing pathways. This is a reasonable mechanistic explanation for why AMD1 deletion would extend lifespan. The reasoning is coherent and biologically sound, though it's somewhat speculative in connecting all the dots (the actual experimental evidence may involve different mechanisms). The confidence level of 0.62 is appropriately calibrated. Overall a strong prediction with good mechanistic reasoning.",
"failure_mode": "correct",
"answer_correct": true,
"mechanism_correct": true,
"reasoning_quality": 4,
"ground_truth_questionable": false
}