madd-2
C. elegans
E3 ubiquitin-protein ligase TRIM9
What the model saw
Gene: madd-2 Organism: Caenorhabditis elegans Known functions: E3 ubiquitin-protein ligase TRIM9. metal ion binding. protein binding. protein homodimerization activity. signaling receptor binding. ubiquitin-protein transferase activity. zinc ion binding.
View unredacted entry
E3 ubiquitin-protein ligase TRIM9. metal ion binding. protein binding. protein homodimerization activity. signaling receptor binding. ubiquitin-protein transferase activity. zinc ion binding.
Solver output
madd-2 encodes a TRIM9 ortholog with E3 ubiquitin-protein ligase activity, functioning in ubiquitin-mediated protein degradation via its RING domain (zinc ion binding). In C. elegans, MADD-2/TRIM9 is primarily characterized as a regulator of axon guidance and synaptic vesicle trafficking through ubiquitination of netrin/UNC-6 pathway components, rather than a canonical longevity pathway regulator. While E3 ligases can influence proteostasis and nutrient sensing, TRIM9-family proteins specifically target cytoskeletal and signaling receptor substrates in neuronal contexts. The protein homodimerization and signaling receptor binding activities suggest roles in modulating receptor turnover at the plasma membrane, but no direct connection to canonical longevity pathways (e.g., IIS, TOR, DAF-16) has been established for this specific ligase. The dual potential to either promote or oppose longevity depending on substrate context makes a confident directional prediction difficult.
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 correctly identified madd-2 as a TRIM9 ortholog with E3 ubiquitin ligase activity and noted its role in axon guidance/netrin signaling, but failed to connect it to longevity regulation. The model was appropriately uncertain given the limited information provided, but ultimately got the answer wrong. The reasoning focused on neuronal/axon guidance functions without identifying the anti-longevity role. The confidence was low (0.38), reflecting genuine uncertainty rather than confident wrongness. The mechanistic reasoning about TRIM9/netrin pathway is partially correct but doesn't capture why madd-2 is anti-longevity in C. elegans.
Raw API responses
solver
{
"reasoning": "madd-2 encodes a TRIM9 ortholog with E3 ubiquitin-protein ligase activity, functioning in ubiquitin-mediated protein degradation via its RING domain (zinc ion binding). In C. elegans, MADD-2/TRIM9 is primarily characterized as a regulator of axon guidance and synaptic vesicle trafficking through ubiquitination of netrin/UNC-6 pathway components, rather than a canonical longevity pathway regulator. While E3 ligases can influence proteostasis and nutrient sensing, TRIM9-family proteins specifically target cytoskeletal and signaling receptor substrates in neuronal contexts. The protein homodimerization and signaling receptor binding activities suggest roles in modulating receptor turnover at the plasma membrane, but no direct connection to canonical longevity pathways (e.g., IIS, TOR, DAF-16) has been established for this specific ligase. The dual potential to either promote or oppose longevity depending on substrate context makes a confident directional prediction difficult.",
"confidence": 0.38,
"key_pathways": [
"UNC-6/Netrin axon guidance signaling",
"Ubiquitin-proteasome system",
"RING-domain E3 ligase substrate ubiquitination"
],
"mechanism_class": "other",
"longevity_influence": "unclear"
}advisor
{
"notes": "The model predicted \"unclear\" while the ground truth is \"anti_longevity.\" The model correctly identified madd-2 as a TRIM9 ortholog with E3 ubiquitin ligase activity and noted its role in axon guidance/netrin signaling, but failed to connect it to longevity regulation. The model was appropriately uncertain given the limited information provided, but ultimately got the answer wrong. The reasoning focused on neuronal/axon guidance functions without identifying the anti-longevity role. The confidence was low (0.38), reflecting genuine uncertainty rather than confident wrongness. The mechanistic reasoning about TRIM9/netrin pathway is partially correct but doesn't capture why madd-2 is anti-longevity in C. elegans.",
"failure_mode": "appropriately_uncertain",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 2,
"ground_truth_questionable": false
}