ARK1
S. cerevisiae
serine/threonine protein kinase ARK1
What the model saw
Gene: ARK1 Organism: Saccharomyces cerevisiae Known functions: serine/threonine protein kinase ARK1. ATP binding. protein binding. protein kinase activity. protein serine kinase activity. protein serine/threonine kinase activity.
View unredacted entry
serine/threonine protein kinase ARK1. ATP binding. protein binding. protein kinase activity. protein serine kinase activity. protein serine/threonine kinase activity.
Solver output
ARK1 (Actin Regulating Kinase 1) is a yeast serine/threonine protein kinase involved in endocytosis and actin cytoskeleton organization, functioning alongside SLA1 and PAN1 to regulate clathrin-mediated endocytosis. While its kinase activity could in principle influence aging-related pathways, the available GO molecular function annotations (ATP binding, protein serine/threonine kinase activity, protein binding) are generic and do not specifically implicate a well-characterized pro- or anti-longevity pathway such as TORC1, sirtuins, or autophagy regulation. ARK1's primary role in endocytic trafficking and actin patch dynamics does not map cleanly to a dominant hallmark of aging in yeast. Without evidence linking ARK1 directly to lifespan regulation (chronological or replicative), the functional annotations alone are insufficient to confidently assign a longevity direction.
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 "anti_longevity." The model's reasoning is coherent and acknowledges the lack of direct evidence linking ARK1 to lifespan regulation, which is a reasonable epistemic stance. However, the prediction is wrong — ARK1 is classified as anti-longevity in GenAge, meaning its deletion likely extends lifespan. The model correctly identified ARK1's role in endocytosis and actin regulation but failed to connect this to a longevity influence. The confidence was appropriately low (0.38), and the model was appropriately uncertain rather than confidently wrong. The reasoning quality is moderate — it's well-articulated but misses the anti-longevity classification.
Raw API responses
solver
{
"reasoning": "ARK1 (Actin Regulating Kinase 1) is a yeast serine/threonine protein kinase involved in endocytosis and actin cytoskeleton organization, functioning alongside SLA1 and PAN1 to regulate clathrin-mediated endocytosis. While its kinase activity could in principle influence aging-related pathways, the available GO molecular function annotations (ATP binding, protein serine/threonine kinase activity, protein binding) are generic and do not specifically implicate a well-characterized pro- or anti-longevity pathway such as TORC1, sirtuins, or autophagy regulation. ARK1's primary role in endocytic trafficking and actin patch dynamics does not map cleanly to a dominant hallmark of aging in yeast. Without evidence linking ARK1 directly to lifespan regulation (chronological or replicative), the functional annotations alone are insufficient to confidently assign a longevity direction.",
"confidence": 0.38,
"key_pathways": [
"clathrin-mediated endocytosis",
"actin cytoskeleton regulation",
"protein serine/threonine phosphorylation"
],
"mechanism_class": "other",
"longevity_influence": "unclear"
}advisor
{
"notes": "The model predicted \"unclear\" while the ground truth is \"anti_longevity.\" The model's reasoning is coherent and acknowledges the lack of direct evidence linking ARK1 to lifespan regulation, which is a reasonable epistemic stance. However, the prediction is wrong — ARK1 is classified as anti-longevity in GenAge, meaning its deletion likely extends lifespan. The model correctly identified ARK1's role in endocytosis and actin regulation but failed to connect this to a longevity influence. The confidence was appropriately low (0.38), and the model was appropriately uncertain rather than confidently wrong. The reasoning quality is moderate — it's well-articulated but misses the anti-longevity classification.",
"failure_mode": "appropriately_uncertain",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 3,
"ground_truth_questionable": false
}