akap-1
C. elegans
KH domain-containing protein akap-1;Tudor domain-containing protein
What the model saw
Gene: akap-1 Organism: Caenorhabditis elegans Known functions: KH domain-containing protein akap-1;Tudor domain-containing protein. RNA binding. nucleic acid binding.
View unredacted entry
KH domain-containing protein akap-1;Tudor domain-containing protein. RNA binding. nucleic acid binding.
Solver output
The akap-1 protein contains KH and Tudor domains, both of which are canonical RNA-binding modules involved in post-transcriptional regulation. KH domains mediate sequence-specific RNA binding and are found in proteins involved in mRNA splicing, stability, and translational control, while Tudor domains recognize methylated arginine/lysine residues and are associated with small RNA (piRNA/siRNA) pathways and germline maintenance. In C. elegans, Tudor-domain proteins are often involved in germline RNA surveillance and transposon silencing, which could relate to genomic stability or proteostasis, but the directionality of longevity influence is not clear from these annotations alone. The broad "RNA binding / nucleic acid binding" annotations do not specify whether this gene promotes or suppresses a pro-longevity pathway, and the combination of KH + Tudor domains could implicate multiple, potentially opposing aging-related mechanisms (e.g., translational repression vs. RNA quality control).
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 about KH and Tudor domain functions is generally accurate in terms of domain biology, but it failed to make a directional prediction. The model was appropriately uncertain given the limited information provided, but it still got the answer wrong. The confidence of 0.35 reflects genuine uncertainty. The mechanistic reasoning about piRNA/siRNA pathways and RNA regulation is plausible but doesn't connect to why akap-1 would be anti-longevity specifically. The model couldn't determine the directionality from the annotations alone, which is understandable but still incorrect.
Raw API responses
solver
{
"reasoning": "The akap-1 protein contains KH and Tudor domains, both of which are canonical RNA-binding modules involved in post-transcriptional regulation. KH domains mediate sequence-specific RNA binding and are found in proteins involved in mRNA splicing, stability, and translational control, while Tudor domains recognize methylated arginine/lysine residues and are associated with small RNA (piRNA/siRNA) pathways and germline maintenance. In C. elegans, Tudor-domain proteins are often involved in germline RNA surveillance and transposon silencing, which could relate to genomic stability or proteostasis, but the directionality of longevity influence is not clear from these annotations alone. The broad \"RNA binding / nucleic acid binding\" annotations do not specify whether this gene promotes or suppresses a pro-longevity pathway, and the combination of KH + Tudor domains could implicate multiple, potentially opposing aging-related mechanisms (e.g., translational repression vs. RNA quality control).",
"confidence": 0.35,
"key_pathways": [
"post-transcriptional RNA regulation",
"small RNA / piRNA pathway (Tudor domain)",
"mRNA binding and translational control (KH domain)"
],
"mechanism_class": "unclear",
"longevity_influence": "unclear"
}advisor
{
"notes": "The model predicted \"unclear\" while the ground truth is \"anti_longevity\". The model's reasoning about KH and Tudor domain functions is generally accurate in terms of domain biology, but it failed to make a directional prediction. The model was appropriately uncertain given the limited information provided, but it still got the answer wrong. The confidence of 0.35 reflects genuine uncertainty. The mechanistic reasoning about piRNA/siRNA pathways and RNA regulation is plausible but doesn't connect to why akap-1 would be anti-longevity specifically. The model couldn't determine the directionality from the annotations alone, which is understandable but still incorrect.",
"failure_mode": "appropriately_uncertain",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 2,
"ground_truth_questionable": false
}