Taxonomic distribution of opsin families inferred from UniProt Reference Proteomes and a suite of opsin-specific hidden Markov models
Bibliographic record
Abstract
Introduction Opsins are a large and sequence-diverse family of light-responsive G-protein coupled receptors involved in vision, circadian rhythm, and other processes. Numerous subfamilies have been defined based on sequence similarity, cell-type localization, signal transduction mechanism, or biological function, but there is no consensus classification system. Methods We used multiple hidden Markov models (HMMs) to identify opsins in the UniProt Reference Proteomes database. Opsin-specific HMMs were also used in an annotation procedure that represents sequences as a vector of HMM scores and assess the similarity of these vectors to those of annotated sequences. UniProt Reference Proteomes are built from genome sequences, allowing us to make meaningful comparisons of the number of opsins in each of the 260 species available at the time of the survey in absolute terms and relative to a larger superfamily of which opsins are a member. Results More than 2,000 opsins were retrieved from 262 species (all metazoans). Discussion Merging opsin counts into higher order taxa paints a broad view of the taxonomic distribution of opsins, and of opsin subfamilies, annotated according to three different schemes.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".