usp-50
C. elegans
ubiquitinyl hydrolase 1
What the model saw
Gene: usp-50 Organism: Caenorhabditis elegans Known functions: ubiquitinyl hydrolase 1. cysteine-type deubiquitinase activity. deubiquitinase activity.
View unredacted entry
ubiquitinyl hydrolase 1. cysteine-type deubiquitinase activity. deubiquitinase activity.
Solver output
USP-50 is a cysteine-type deubiquitinase (DUB) belonging to the ubiquitin-specific protease (USP) family, which removes ubiquitin chains from substrate proteins and thereby modulates their stability, localization, or activity. DUBs can either promote or oppose longevity depending on their specific substrates: some DUBs stabilize pro-longevity factors (e.g., DAF-16/FOXO, stress response proteins) while others stabilize pro-aging or growth-promoting factors. Without knowledge of usp-50's specific substrates in C. elegans, the net effect on proteostasis and aging is ambiguous. The ubiquitin-proteasome system is central to proteostasis maintenance, a key hallmark of aging, but the directionality here cannot be resolved from molecular function annotations alone.
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 "unclear" while the ground truth is "pro_longevity." The model's reasoning is logically sound given the limited information provided - it correctly identifies USP-50 as a deubiquitinase and notes that DUBs can have variable effects on longevity depending on their substrates. The model appropriately expressed uncertainty (confidence 0.38) rather than making a confident wrong prediction. However, the answer is still incorrect. The mechanism class of "loss_of_proteostasis" is somewhat misapplied here - the model is discussing proteostasis regulation generally, not specifically loss of proteostasis. The model could not determine the pro-longevity direction from the annotations alone, which is a reasonable limitation but still results in a wrong answer.
Raw API responses
solver
{
"reasoning": "USP-50 is a cysteine-type deubiquitinase (DUB) belonging to the ubiquitin-specific protease (USP) family, which removes ubiquitin chains from substrate proteins and thereby modulates their stability, localization, or activity. DUBs can either promote or oppose longevity depending on their specific substrates: some DUBs stabilize pro-longevity factors (e.g., DAF-16/FOXO, stress response proteins) while others stabilize pro-aging or growth-promoting factors. Without knowledge of usp-50's specific substrates in C. elegans, the net effect on proteostasis and aging is ambiguous. The ubiquitin-proteasome system is central to proteostasis maintenance, a key hallmark of aging, but the directionality here cannot be resolved from molecular function annotations alone.",
"confidence": 0.38,
"key_pathways": [
"ubiquitin-proteasome system",
"deubiquitination",
"proteostasis regulation"
],
"mechanism_class": "loss_of_proteostasis",
"longevity_influence": "unclear"
}advisor
{
"notes": "The model predicted \"unclear\" while the ground truth is \"pro_longevity.\" The model's reasoning is logically sound given the limited information provided - it correctly identifies USP-50 as a deubiquitinase and notes that DUBs can have variable effects on longevity depending on their substrates. The model appropriately expressed uncertainty (confidence 0.38) rather than making a confident wrong prediction. However, the answer is still incorrect. The mechanism class of \"loss_of_proteostasis\" is somewhat misapplied here - the model is discussing proteostasis regulation generally, not specifically loss of proteostasis. The model could not determine the pro-longevity direction from the annotations alone, which is a reasonable limitation but still results in a wrong answer.",
"failure_mode": "appropriately_uncertain",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 3,
"ground_truth_questionable": false
}