DBP3
S. cerevisiae
RNA-dependent ATPase DBP3
What the model saw
Gene: DBP3 Organism: Saccharomyces cerevisiae Known functions: RNA-dependent ATPase DBP3. ATP binding. ATP hydrolysis activity. ATP-dependent activity, acting on RNA. RNA helicase activity. catalytic activity, acting on RNA. helicase activity. mRNA binding. nucleic acid binding.
View unredacted entry
RNA-dependent ATPase DBP3. ATP binding. ATP hydrolysis activity. ATP-dependent activity, acting on RNA. RNA helicase activity. catalytic activity, acting on RNA. helicase activity. mRNA binding. nucleic acid binding.
Solver output
DBP3 is a DEAD-box RNA helicase that uses ATP hydrolysis to remodel RNA secondary structures, and is known to function in ribosome biogenesis — specifically in pre-rRNA processing and assembly of the large ribosomal subunit. Efficient ribosome biogenesis is essential for maintaining translational fidelity and proteostasis; defects in this process lead to aberrant protein synthesis and accumulation of misfolded proteins. RNA helicases in the DEAD-box family that support ribosome assembly are generally required for normal cellular fitness and lifespan in yeast. Loss of DBP3 function impairs rRNA processing, reducing the quality and quantity of functional ribosomes, which compromises proteostasis and is expected to shorten lifespan. Therefore, the normal function of DBP3 is predicted to be pro-longevity by supporting ribosome biogenesis and translational accuracy.
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. DBP3 is actually an anti-longevity gene in yeast, meaning its deletion extends lifespan. The model's reasoning assumed that because DBP3 supports ribosome biogenesis, its loss would be harmful and shorten lifespan. However, this is a common error: reduced ribosome biogenesis is actually associated with lifespan extension in yeast (consistent with TOR pathway inhibition and dietary restriction effects). The model's mechanistic reasoning about ribosome biogenesis is partially correct in terms of DBP3's function, but the conclusion drawn from it is backwards. The model had moderate confidence (0.62) but was still wrong. The reasoning quality is low because it failed to account for the well-established connection between reduced ribosome biogenesis/translation and longevity extension in yeast.
Raw API responses
solver
{
"reasoning": "DBP3 is a DEAD-box RNA helicase that uses ATP hydrolysis to remodel RNA secondary structures, and is known to function in ribosome biogenesis — specifically in pre-rRNA processing and assembly of the large ribosomal subunit. Efficient ribosome biogenesis is essential for maintaining translational fidelity and proteostasis; defects in this process lead to aberrant protein synthesis and accumulation of misfolded proteins. RNA helicases in the DEAD-box family that support ribosome assembly are generally required for normal cellular fitness and lifespan in yeast. Loss of DBP3 function impairs rRNA processing, reducing the quality and quantity of functional ribosomes, which compromises proteostasis and is expected to shorten lifespan. Therefore, the normal function of DBP3 is predicted to be pro-longevity by supporting ribosome biogenesis and translational accuracy.",
"confidence": 0.62,
"key_pathways": [
"ribosome biogenesis",
"pre-rRNA processing",
"translational fidelity/proteostasis"
],
"mechanism_class": "loss_of_proteostasis",
"longevity_influence": "pro_longevity"
}advisor
{
"notes": "The model predicted pro_longevity but the ground truth is anti_longevity. DBP3 is actually an anti-longevity gene in yeast, meaning its deletion extends lifespan. The model's reasoning assumed that because DBP3 supports ribosome biogenesis, its loss would be harmful and shorten lifespan. However, this is a common error: reduced ribosome biogenesis is actually associated with lifespan extension in yeast (consistent with TOR pathway inhibition and dietary restriction effects). The model's mechanistic reasoning about ribosome biogenesis is partially correct in terms of DBP3's function, but the conclusion drawn from it is backwards. The model had moderate confidence (0.62) but was still wrong. The reasoning quality is low because it failed to account for the well-established connection between reduced ribosome biogenesis/translation and longevity extension in yeast.",
"failure_mode": "confident_wrong",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 2,
"ground_truth_questionable": false
}