skr-5
C. elegans
Skp1-related protein
What the model saw
Gene: skr-5 Organism: Caenorhabditis elegans Known functions: Skp1-related protein. cullin family protein binding.
View unredacted entry
Skp1-related protein. cullin family protein binding.
Solver output
SKR-5 is a Skp1-related protein in C. elegans that binds cullin family proteins, placing it as an adaptor subunit of SCF (Skp1-Cullin-F-box) E3 ubiquitin ligase complexes. SCF complexes mediate ubiquitin-dependent proteasomal degradation of specific substrates, which is central to proteostasis. However, the specific F-box protein partner(s) and substrates of SKR-5 are not defined by these annotations alone. C. elegans encodes ~21 skr paralogs with distinct substrate specificities; without knowing which substrates SKR-5 targets for degradation, it is impossible to determine whether its activity promotes or opposes longevity pathways (e.g., degrading pro-longevity vs. anti-longevity factors). The function is consistent with proteostasis regulation but the directionality remains ambiguous.
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 is logically sound given the limited information provided - it correctly identifies SKR-5 as an SCF complex adaptor and notes the ambiguity in directionality without knowing specific substrates. However, the model failed to arrive at the correct answer. The mechanism class of "loss_of_proteostasis" is speculative and not confirmed. The model's uncertainty was appropriate given the sparse annotation, but it still got the answer wrong. This is a case of appropriate uncertainty rather than confident wrongness.
Raw API responses
solver
{
"reasoning": "SKR-5 is a Skp1-related protein in C. elegans that binds cullin family proteins, placing it as an adaptor subunit of SCF (Skp1-Cullin-F-box) E3 ubiquitin ligase complexes. SCF complexes mediate ubiquitin-dependent proteasomal degradation of specific substrates, which is central to proteostasis. However, the specific F-box protein partner(s) and substrates of SKR-5 are not defined by these annotations alone. C. elegans encodes ~21 skr paralogs with distinct substrate specificities; without knowing which substrates SKR-5 targets for degradation, it is impossible to determine whether its activity promotes or opposes longevity pathways (e.g., degrading pro-longevity vs. anti-longevity factors). The function is consistent with proteostasis regulation but the directionality remains ambiguous.",
"confidence": 0.35,
"key_pathways": [
"SCF E3 ubiquitin ligase complex",
"ubiquitin-proteasome system",
"cullin-RING ligase pathway"
],
"mechanism_class": "loss_of_proteostasis",
"longevity_influence": "unclear"
}advisor
{
"notes": "The model predicted \"unclear\" while the ground truth is \"anti_longevity.\" The model's reasoning is logically sound given the limited information provided - it correctly identifies SKR-5 as an SCF complex adaptor and notes the ambiguity in directionality without knowing specific substrates. However, the model failed to arrive at the correct answer. The mechanism class of \"loss_of_proteostasis\" is speculative and not confirmed. The model's uncertainty was appropriate given the sparse annotation, but it still got the answer wrong. This is a case of appropriate uncertainty rather than confident wrongness.",
"failure_mode": "appropriately_uncertain",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 3,
"ground_truth_questionable": false
}