cyk-3
C. elegans
Ubiquitin carboxyl-terminal hydrolase cyk-3
What the model saw
Gene: cyk-3 Organism: Caenorhabditis elegans Known functions: Ubiquitin carboxyl-terminal hydrolase cyk-3. calcium ion binding. cysteine-type deubiquitinase activity.
View unredacted entry
Ubiquitin carboxyl-terminal hydrolase cyk-3. calcium ion binding. cysteine-type deubiquitinase activity.
Solver output
CYK-3 is a cysteine-type deubiquitinase (DUB), meaning its normal function is to remove ubiquitin chains from substrate proteins, thereby rescuing them from proteasomal degradation or modulating ubiquitin signaling. Proper deubiquitinase activity is essential for maintaining proteostasis by regulating ubiquitin pool availability, editing ubiquitin chain topology, and preventing aberrant degradation of functional proteins. In C. elegans, robust proteostasis—including balanced ubiquitin-proteasome system (UPS) activity—is a well-established pro-longevity mechanism. Deubiquitinases that support UPS fidelity and ubiquitin recycling tend to promote longevity by preventing accumulation of misfolded or aggregated proteins. The calcium ion binding activity may additionally link CYK-3 to calcium-dependent signaling that modulates stress responses. Overall, the deubiquitinase function of CYK-3 most plausibly supports proteostasis maintenance, placing it in the pro-longevity category.
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 pro_longevity but the ground truth is anti_longevity. The model's reasoning is based on a general assumption that deubiquitinases support proteostasis and therefore promote longevity, but this is an oversimplification. The model did not consider that cyk-3 could be anti-longevity — for example, if its deubiquitinase activity stabilizes proteins that limit lifespan, or if its loss-of-function extends lifespan. The model's confidence of 0.62 is moderate but still wrong. The mechanistic reasoning is plausible in general terms but incorrect for this specific gene, and the model failed to consider the anti-longevity possibility seriously.
Raw API responses
solver
{
"reasoning": "CYK-3 is a cysteine-type deubiquitinase (DUB), meaning its normal function is to remove ubiquitin chains from substrate proteins, thereby rescuing them from proteasomal degradation or modulating ubiquitin signaling. Proper deubiquitinase activity is essential for maintaining proteostasis by regulating ubiquitin pool availability, editing ubiquitin chain topology, and preventing aberrant degradation of functional proteins. In C. elegans, robust proteostasis—including balanced ubiquitin-proteasome system (UPS) activity—is a well-established pro-longevity mechanism. Deubiquitinases that support UPS fidelity and ubiquitin recycling tend to promote longevity by preventing accumulation of misfolded or aggregated proteins. The calcium ion binding activity may additionally link CYK-3 to calcium-dependent signaling that modulates stress responses. Overall, the deubiquitinase function of CYK-3 most plausibly supports proteostasis maintenance, placing it in the pro-longevity category.",
"confidence": 0.62,
"key_pathways": [
"ubiquitin-proteasome system",
"deubiquitination and ubiquitin recycling",
"proteostasis maintenance"
],
"mechanism_class": "loss_of_proteostasis",
"longevity_influence": "pro_longevity"
}advisor
{
"notes": "The model predicted pro_longevity but the ground truth is anti_longevity. The model's reasoning is based on a general assumption that deubiquitinases support proteostasis and therefore promote longevity, but this is an oversimplification. The model did not consider that cyk-3 could be anti-longevity — for example, if its deubiquitinase activity stabilizes proteins that limit lifespan, or if its loss-of-function extends lifespan. The model's confidence of 0.62 is moderate but still wrong. The mechanistic reasoning is plausible in general terms but incorrect for this specific gene, and the model failed to consider the anti-longevity possibility seriously.",
"failure_mode": "confident_wrong",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 2,
"ground_truth_questionable": false
}