nnk1

S. pombe

serine/threonine protein kinase Nnk1

What the model saw

Gene: nnk1
Organism: Schizosaccharomyces pombe
Known functions: serine/threonine protein kinase Nnk1. ATP binding. protein kinase activity. protein serine kinase activity. protein serine/threonine kinase activity.

View unredacted entry

serine/threonine protein kinase Nnk1. ATP binding. protein kinase activity. protein serine kinase activity. protein serine/threonine kinase activity.

Solver output

Predicted influence

Unclear

Confidence

35%

Mechanism

Deregulated nutrient sensing

Reasoning

Nnk1 is a serine/threonine protein kinase in S. pombe with ATP-binding activity, placing it within the broad class of kinase signaling regulators. Serine/threonine kinases in yeast frequently participate in nutrient-sensing pathways (e.g., TORC1, AMPK, or stress-response cascades) that are central regulators of longevity. However, the specific substrates and upstream regulators of Nnk1 are not defined by the provided annotations, making it impossible to determine whether its activity promotes or opposes longevity-associated signaling. Without knowledge of whether Nnk1 activates pro-growth/anti-autophagy pathways (anti-longevity) or stress-response/pro-survival pathways (pro-longevity), the directionality of its influence on lifespan remains ambiguous. The generic kinase annotation alone is insufficient to resolve this conflict.

Key pathways

serine/threonine kinase signalingnutrient sensingstress response kinase cascades

Longevity influence

Anti-longevity

Lifespan effect

Increase

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

Answer

✗Incorrect

Mechanism

✗Incorrect

Reasoning quality

2/5

Failure mode

Appropriately uncertain

Notes

The model predicted "unclear" with low confidence (0.35), while the ground truth is "anti_longevity." The model's reasoning is generic - it correctly identifies Nnk1 as a serine/threonine kinase and speculates about possible nutrient-sensing roles, but cannot determine directionality. The model was appropriately uncertain given the limited information provided, but ultimately got the answer wrong. The mechanism class of "deregulated_nutrient_sensing" is speculative and unverified. The model's hedging was reasonable given the sparse annotation, but the prediction of "unclear" does not match the ground truth of "anti_longevity."

Raw API responses

solver

{
  "reasoning": "Nnk1 is a serine/threonine protein kinase in S. pombe with ATP-binding activity, placing it within the broad class of kinase signaling regulators. Serine/threonine kinases in yeast frequently participate in nutrient-sensing pathways (e.g., TORC1, AMPK, or stress-response cascades) that are central regulators of longevity. However, the specific substrates and upstream regulators of Nnk1 are not defined by the provided annotations, making it impossible to determine whether its activity promotes or opposes longevity-associated signaling. Without knowledge of whether Nnk1 activates pro-growth/anti-autophagy pathways (anti-longevity) or stress-response/pro-survival pathways (pro-longevity), the directionality of its influence on lifespan remains ambiguous. The generic kinase annotation alone is insufficient to resolve this conflict.",
  "confidence": 0.35,
  "key_pathways": [
    "serine/threonine kinase signaling",
    "nutrient sensing",
    "stress response kinase cascades"
  ],
  "mechanism_class": "deregulated_nutrient_sensing",
  "longevity_influence": "unclear"
}

advisor

{
  "notes": "The model predicted \"unclear\" with low confidence (0.35), while the ground truth is \"anti_longevity.\" The model's reasoning is generic - it correctly identifies Nnk1 as a serine/threonine kinase and speculates about possible nutrient-sensing roles, but cannot determine directionality. The model was appropriately uncertain given the limited information provided, but ultimately got the answer wrong. The mechanism class of \"deregulated_nutrient_sensing\" is speculative and unverified. The model's hedging was reasonable given the sparse annotation, but the prediction of \"unclear\" does not match the ground truth of \"anti_longevity.\"",
  "failure_mode": "appropriately_uncertain",
  "answer_correct": false,
  "mechanism_correct": false,
  "reasoning_quality": 2,
  "ground_truth_questionable": false
}