cyp-13B1
C. elegans
Putative cytochrome P450 cyp-13B1
What the model saw
Gene: cyp-13B1 Organism: Caenorhabditis elegans Known functions: Putative cytochrome P450 cyp-13B1. heme binding. iron ion binding. monooxygenase activity. oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen.
View unredacted entry
Putative cytochrome P450 cyp-13B1. heme binding. iron ion binding. monooxygenase activity. oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen.
Solver output
cyp-13B1 encodes a putative cytochrome P450 monooxygenase in C. elegans, characterized by heme binding, iron ion binding, and oxidoreductase/monooxygenase activity. CYP450 enzymes in C. elegans can serve diverse roles including xenobiotic detoxification, lipid/sterol metabolism, and biosynthesis of signaling molecules such as dafachronic acids (DAF-12 ligands), which are pro-longevity. However, cyp-13B1 belongs to the CYP-13 family, which is not among the well-characterized dafachronic acid-synthesizing CYPs (e.g., daf-9/CYP22A1). Without specific substrate or pathway information, the direction of its influence on longevity—whether through detoxification, lipid remodeling, or steroid hormone signaling—cannot be confidently assigned. The monooxygenase activity could either generate or detoxify reactive intermediates, creating genuinely conflicting possibilities for aging outcomes.
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 reasonable given the limited information provided - it correctly identifies cyp-13B1 as a cytochrome P450 and discusses possible roles, but fails to commit to a direction. The model's uncertainty is understandable given the sparse functional annotation, but it missed the anti-longevity classification. The reasoning about CYP450 diversity and the inability to assign direction without substrate/pathway information is logically sound, but ultimately incorrect in outcome. The model appropriately noted that cyp-13B1 is not among the well-characterized dafachronic acid-synthesizing CYPs, which shows some domain knowledge. However, the model could not determine the anti-longevity role from the available information.
Raw API responses
solver
{
"reasoning": "cyp-13B1 encodes a putative cytochrome P450 monooxygenase in C. elegans, characterized by heme binding, iron ion binding, and oxidoreductase/monooxygenase activity. CYP450 enzymes in C. elegans can serve diverse roles including xenobiotic detoxification, lipid/sterol metabolism, and biosynthesis of signaling molecules such as dafachronic acids (DAF-12 ligands), which are pro-longevity. However, cyp-13B1 belongs to the CYP-13 family, which is not among the well-characterized dafachronic acid-synthesizing CYPs (e.g., daf-9/CYP22A1). Without specific substrate or pathway information, the direction of its influence on longevity—whether through detoxification, lipid remodeling, or steroid hormone signaling—cannot be confidently assigned. The monooxygenase activity could either generate or detoxify reactive intermediates, creating genuinely conflicting possibilities for aging outcomes.",
"confidence": 0.38,
"key_pathways": [
"cytochrome P450 monooxygenase activity",
"heme/iron-dependent oxidoreduction",
"lipid/sterol metabolism"
],
"mechanism_class": "other",
"longevity_influence": "unclear"
}advisor
{
"notes": "The model predicted \"unclear\" while the ground truth is \"anti_longevity.\" The model's reasoning is reasonable given the limited information provided - it correctly identifies cyp-13B1 as a cytochrome P450 and discusses possible roles, but fails to commit to a direction. The model's uncertainty is understandable given the sparse functional annotation, but it missed the anti-longevity classification. The reasoning about CYP450 diversity and the inability to assign direction without substrate/pathway information is logically sound, but ultimately incorrect in outcome. The model appropriately noted that cyp-13B1 is not among the well-characterized dafachronic acid-synthesizing CYPs, which shows some domain knowledge. However, the model could not determine the anti-longevity role from the available information.",
"failure_mode": "appropriately_uncertain",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 3,
"ground_truth_questionable": false
}