DUF1070 as a signature domain of a subclass of arabinogalactan peptides
Bibliographic record
Abstract
Over 20% of all protein domains are currently annotated as ?domains of unknown function? or DUFs. In a recently identified Centaurium erythraea arabinogalactan peptide, CeAGP3 (AGN92423), a conserved DUF1070 domain was found. Since identifying functions for DUFs is important in systems biology, we have analyzed the distribution and structure of DUF1070 domain (pfam06376) using a set of bioinformatics tools. There are 271 publically available DUF1070 members from 25 diverse families of vascular plants, and most are short sequences (50-100 aa). The N-terminal signal peptide (Nsp) was found in almost all complete sequences. In 233 sequences, at least two noncontiguous prolines were found as clustered dipeptides predicted to be hydroxylated and glycosylated with type II arabino-3,6-galactans, thus representing AG-II glycomodules. In addition, 35 sequences contained a region rich in basic residues (basic linker, BL). The N-terminal part of the DUF1070 domain is comprised of (part of) AG-II and/or BL, while the highly conserved C-terminus is a region of 26 aa, termed SH26. In 212 sequences, SH26 was a typical glycosylphosphatidylinositol lipid anchor signal peptide (GPIsp), but in 83 cases GPIsp was not predicted due to software constraints. In sequences where both Nsp and GPIsp were predicted, the length of mature peptides could be calculated, and it was 10-16 aa. Our analysis suggests that DUF1070 members are arabinogalactan (AG) peptides, of which the majority are GPI-anchored. DUF1070 is the only conserved domain found in classical arabinogalactan proteins and AG peptides. The SH26 region can be used for mining and annotation of AG peptides.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.002 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 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".