Supplementary Dataset for Saeed et al. 2021: Evolution and Functions of Plant U-box proteins (PUBs): From protein quality control to signalling
Bibliographic record
Abstract
This record contains additional information and a supplementary dataset of sequence alignment files and phylograms that support the publication: Saeed B, Trenner J, Monaghan J, Quint M, Shabek N, Trujillo M. 2021. Evolution and Functions of Plant U-box proteins (PUBs): From protein quality control to signalling. (submitted to Annual Review of Plant Biology) included files: Additional information.pdf This file contains Supplementary Methods and References for the phylogenetic analyses. Ubox_full_protein_maximum_likelihood_phylogram_linear.pdf A multiple protein sequence alignment by MAFFT (22) of 1121 U-box protein sequences from 21 species and four outgroup sequences containing a RING finger domain (A. thaliana RBX1, A. thaliana RMA1, S. cerevisiae RAD18, Homo sapiens TRAF6 ) was used to infer a phylogenetic tree by maximum likelihood with IQ-TREE (31, 32). The implemented ultrafast bootstrap approximation, set to 2000 bootstrap samples, was used for branch support (17). The consensus tree was annotated using iTOL (25). Ubox_domain_maximum_likelihood_phylogram_linear.pdf In order to analyse specifically the evolution of the U-box domain, the U-box domain of the final 1121 U-box protein sequences as well as the RING finger domain of the four outgroup sequences were isolated and aligned by MAFFT (22). The U-box domain alignment was then used to infer a phylogenetic tree by maximum likelihood with IQ-TREE (31, 32). The implemented ultrafast bootstrap approximation, set to 2000 bootstrap samples, was used for branch support (17). The consensus tree was annotated using iTOL (25). This tree was used to interpret the evolutionary history of U-box proteins in the main text. MAFFT_alignment _1121seqs_Ubox_full_protein_plus_4seqs_RING_outgroup.fasta Multiple protein sequences alignment by MAFFT (22) of 1121 U-box full length protein sequences and four RING finger protein sequences, FASTA formatted. MAFFT_alignment _1121seqs_Ubox_domain_plus_4seqs_RING_outgroup.fasta Multiple protein sequences alignment by MAFFT (22) of U-box domain sequences of 1121 U-box protein and four RING finger domain sequences of outgroup sequences, FASTA formatted. Ubox_protein_sequences_information.xlsx Spreadsheet with sequence ID information and source databases.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.015 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.004 | 0.008 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.003 | 0.003 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.003 | 0.002 |
| Insufficient payload (model declined to judge) | 0.671 | 0.325 |
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 source (direct Gemma or distilled Codex), 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".