PMT7
S. cerevisiae
putative dolichyl-phosphate-mannose--protein mannosyltransferase
What the model saw
Gene: PMT7 Organism: Saccharomyces cerevisiae Known functions: putative dolichyl-phosphate-mannose--protein mannosyltransferase. dolichyl-phosphate-mannose-protein mannosyltransferase activity. mannosyltransferase activity.
View unredacted entry
putative dolichyl-phosphate-mannose--protein mannosyltransferase. dolichyl-phosphate-mannose-protein mannosyltransferase activity. mannosyltransferase activity.
Solver output
PMT7 encodes a putative dolichyl-phosphate-mannose–protein mannosyltransferase (PMT family), which catalyzes O-mannosylation of serine/threonine residues on secretory and membrane proteins in the ER. O-mannosylation is critical for proper protein folding, stability, and quality control in the secretory pathway, linking it to proteostasis. While other PMT family members (PMT1, PMT2, PMT4) have established roles in cell wall integrity and protein glycosylation, PMT7 is annotated as "putative" with limited functional characterization, suggesting partial or redundant activity. Loss of O-mannosylation can trigger ER stress and UPR activation, which has complex and context-dependent effects on longevity. The redundancy within the PMT family and the putative/unconfirmed nature of PMT7's enzymatic activity make it difficult to assign a clear pro- or anti-longevity role.
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 PMT7's putative nature and redundancy within the PMT family led it to hedge rather than commit to a direction. While the mechanistic reasoning about O-mannosylation, ER stress, and proteostasis is plausible, the model failed to recognize that deletion of PMT7 likely extends lifespan (anti_longevity = the gene works against longevity, meaning its deletion promotes longevity). The model's uncertainty was somewhat reasonable given PMT7's "putative" annotation, but it still missed the correct classification. The mechanism class of "loss_of_proteostasis" is not clearly wrong but is also not well-supported as the primary mechanism for PMT7's anti-longevity role.
Raw API responses
solver
{
"reasoning": "PMT7 encodes a putative dolichyl-phosphate-mannose–protein mannosyltransferase (PMT family), which catalyzes O-mannosylation of serine/threonine residues on secretory and membrane proteins in the ER. O-mannosylation is critical for proper protein folding, stability, and quality control in the secretory pathway, linking it to proteostasis. While other PMT family members (PMT1, PMT2, PMT4) have established roles in cell wall integrity and protein glycosylation, PMT7 is annotated as \"putative\" with limited functional characterization, suggesting partial or redundant activity. Loss of O-mannosylation can trigger ER stress and UPR activation, which has complex and context-dependent effects on longevity. The redundancy within the PMT family and the putative/unconfirmed nature of PMT7's enzymatic activity make it difficult to assign a clear pro- or anti-longevity role.",
"confidence": 0.38,
"key_pathways": [
"O-mannosylation / dolichyl-phosphate-mannose transfer",
"ER protein quality control / UPR",
"cell wall integrity signaling"
],
"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 about PMT7's putative nature and redundancy within the PMT family led it to hedge rather than commit to a direction. While the mechanistic reasoning about O-mannosylation, ER stress, and proteostasis is plausible, the model failed to recognize that deletion of PMT7 likely extends lifespan (anti_longevity = the gene works against longevity, meaning its deletion promotes longevity). The model's uncertainty was somewhat reasonable given PMT7's \"putative\" annotation, but it still missed the correct classification. The mechanism class of \"loss_of_proteostasis\" is not clearly wrong but is also not well-supported as the primary mechanism for PMT7's anti-longevity role.",
"failure_mode": "appropriately_uncertain",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 2,
"ground_truth_questionable": false
}