YVH1
S. cerevisiae
tyrosine protein phosphatase YVH1
What the model saw
Gene: YVH1 Organism: Saccharomyces cerevisiae Known functions: tyrosine protein phosphatase YVH1. catalytic activity, acting on a protein. phosphatase activity. preribosome binding. protein binding. protein tyrosine phosphatase activity. protein tyrosine/serine/threonine phosphatase activity.
View unredacted entry
tyrosine protein phosphatase YVH1. catalytic activity, acting on a protein. phosphatase activity. preribosome binding. protein binding. protein tyrosine phosphatase activity. protein tyrosine/serine/threonine phosphatase activity.
Solver output
YVH1 is a dual-specificity protein phosphatase (tyrosine/serine/threonine) in S. cerevisiae that binds to preribosomes and participates in ribosome biogenesis and maturation. Its phosphatase activity on ribosomal assembly factors is required for proper 60S subunit maturation, linking it to translational capacity regulation. Reduced or dysregulated ribosome biogenesis and translation are associated with extended lifespan in yeast (e.g., deletion of large ribosomal subunit genes extends chronological and replicative lifespan), suggesting that YVH1's role in promoting efficient ribosome assembly and translation is part of the nutrient-sensing/TOR signaling axis. YVH1 has also been implicated in counteracting stress responses and modulating TORC1-related signaling through its phosphatase activity, placing it in the deregulated nutrient-sensing hallmark. Because active ribosome biogenesis and high translational output are generally associated with pro-growth, pro-aging states, YVH1's normal function in facilitating these processes would tend to promote aging rather than longevity; however, its role as a phosphatase that fine-tunes ribosomal assembly could also serve a quality-control function that supports proteostasis and longevity.
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 pro_longevity but the ground truth is anti_longevity. The model's reasoning about YVH1's role in ribosome biogenesis and TOR signaling is partially relevant, but the model ultimately drew the wrong conclusion. Interestingly, the model's own reasoning hints at the correct answer ("YVH1's normal function in facilitating these processes would tend to promote aging rather than longevity"), but then hedged and chose pro_longevity anyway. The mechanism class of "deregulated_nutrient_sensing" is speculative and not well-supported. The model contradicted itself in its own reasoning but still chose the wrong answer. Confidence of 0.62 is moderate but still wrong.
Raw API responses
solver
{
"reasoning": "YVH1 is a dual-specificity protein phosphatase (tyrosine/serine/threonine) in S. cerevisiae that binds to preribosomes and participates in ribosome biogenesis and maturation. Its phosphatase activity on ribosomal assembly factors is required for proper 60S subunit maturation, linking it to translational capacity regulation. Reduced or dysregulated ribosome biogenesis and translation are associated with extended lifespan in yeast (e.g., deletion of large ribosomal subunit genes extends chronological and replicative lifespan), suggesting that YVH1's role in promoting efficient ribosome assembly and translation is part of the nutrient-sensing/TOR signaling axis. YVH1 has also been implicated in counteracting stress responses and modulating TORC1-related signaling through its phosphatase activity, placing it in the deregulated nutrient-sensing hallmark. Because active ribosome biogenesis and high translational output are generally associated with pro-growth, pro-aging states, YVH1's normal function in facilitating these processes would tend to promote aging rather than longevity; however, its role as a phosphatase that fine-tunes ribosomal assembly could also serve a quality-control function that supports proteostasis and longevity.",
"confidence": 0.62,
"key_pathways": [
"ribosome biogenesis and 60S subunit maturation",
"TOR/nutrient-sensing signaling",
"protein phosphatase regulation of translation"
],
"mechanism_class": "deregulated_nutrient_sensing",
"longevity_influence": "pro_longevity"
}advisor
{
"notes": "The model predicted pro_longevity but the ground truth is anti_longevity. The model's reasoning about YVH1's role in ribosome biogenesis and TOR signaling is partially relevant, but the model ultimately drew the wrong conclusion. Interestingly, the model's own reasoning hints at the correct answer (\"YVH1's normal function in facilitating these processes would tend to promote aging rather than longevity\"), but then hedged and chose pro_longevity anyway. The mechanism class of \"deregulated_nutrient_sensing\" is speculative and not well-supported. The model contradicted itself in its own reasoning but still chose the wrong answer. Confidence of 0.62 is moderate but still wrong.",
"failure_mode": "confident_wrong",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 2,
"ground_truth_questionable": false
}