t25b9.1
C. elegans
Aminotransferase class I/classII large domain-containing protein
What the model saw
Gene: T25B9.1 Organism: Caenorhabditis elegans Known functions: Aminotransferase class I/classII large domain-containing protein. glycine C-acetyltransferase activity. pyridoxal phosphate binding.
View unredacted entry
Aminotransferase class I/classII large domain-containing protein. glycine C-acetyltransferase activity. pyridoxal phosphate binding.
Solver output
T25B9.1 encodes a pyridoxal phosphate (PLP)-dependent aminotransferase with glycine C-acetyltransferase activity, catalyzing the condensation of glycine with acetyl-CoA to produce 2-amino-3-ketobutyrate, a step in threonine catabolism and one-carbon/amino acid metabolism. While glycine metabolism has been linked to longevity (glycine supplementation extends lifespan in some models), the specific enzymatic step here—glycine C-acetyltransferase—consumes glycine rather than producing it, which could theoretically reduce glycine availability and oppose pro-longevity glycine signaling. However, this reaction also feeds into central metabolic pathways (acetyl-CoA utilization, amino acid homeostasis) whose net effect on aging in C. elegans is not clearly established. The PLP-binding aminotransferase class I/II domain suggests broad substrate flexibility, making it difficult to assign a definitive pro- or anti-longevity role without direct lifespan data.
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 confidence was low (0.38), and it acknowledged uncertainty, but it still failed to arrive at the correct answer. The mechanistic reasoning about glycine C-acetyltransferase consuming glycine and potentially opposing pro-longevity glycine signaling is speculative and not well-supported. The model did not identify the anti-longevity role of this gene. While the model's uncertainty is somewhat appropriate given limited direct evidence, it still missed the correct classification entirely.
Raw API responses
solver
{
"reasoning": "T25B9.1 encodes a pyridoxal phosphate (PLP)-dependent aminotransferase with glycine C-acetyltransferase activity, catalyzing the condensation of glycine with acetyl-CoA to produce 2-amino-3-ketobutyrate, a step in threonine catabolism and one-carbon/amino acid metabolism. While glycine metabolism has been linked to longevity (glycine supplementation extends lifespan in some models), the specific enzymatic step here—glycine C-acetyltransferase—consumes glycine rather than producing it, which could theoretically reduce glycine availability and oppose pro-longevity glycine signaling. However, this reaction also feeds into central metabolic pathways (acetyl-CoA utilization, amino acid homeostasis) whose net effect on aging in C. elegans is not clearly established. The PLP-binding aminotransferase class I/II domain suggests broad substrate flexibility, making it difficult to assign a definitive pro- or anti-longevity role without direct lifespan data.",
"confidence": 0.38,
"key_pathways": [
"glycine metabolism / one-carbon metabolism",
"threonine catabolism via glycine C-acetyltransferase",
"pyridoxal phosphate-dependent amino acid metabolism"
],
"mechanism_class": "deregulated_nutrient_sensing",
"longevity_influence": "unclear"
}advisor
{
"notes": "The model predicted \"unclear\" while the ground truth is \"anti_longevity.\" The model's confidence was low (0.38), and it acknowledged uncertainty, but it still failed to arrive at the correct answer. The mechanistic reasoning about glycine C-acetyltransferase consuming glycine and potentially opposing pro-longevity glycine signaling is speculative and not well-supported. The model did not identify the anti-longevity role of this gene. While the model's uncertainty is somewhat appropriate given limited direct evidence, it still missed the correct classification entirely.",
"failure_mode": "appropriately_uncertain",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 2,
"ground_truth_questionable": false
}