Rv1374c Still unknown · low auto-curated
H37Rv Rv1374c · MTBC0 mtbc0_001475 ·
152 aa · 1556416–1556874 (-) ·
RefSeq NP_215890.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 7x75-assembly1_D Cryo-EM structure of Streptomyces coelicolor RNAP-pro (prob 0.04, TM 0.33). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71802
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein |
UniProt still lists this protein as Uncharacterized protein; the revised annotation above is ahead of the current UniProt record.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 2.076 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 6 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.10% of strains (148) · clonal |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 55.4 (low). Low-confidence model: the fold may be unreliable, so treat these structural hits with caution.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
7x75-assembly1_D |
0.04 | 0.33 | 8.3e+00 | 7x75-assembly1_D Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open complex with three Zur dimers |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1375 hyp |
hypothetical protein | 405 | 405 ctx | neighborhood:401 |
Rv1376 hyp |
hypothetical protein | 490 | 403 ctx | neighborhood:401 |
Rv0046c ino1 |
inositol-3-phosphate synthase | 550 | 55 | textmining:544 |
Rv1954c hyp |
hypothetical protein | 521 | 55 | textmining:514 |
Rv1805c hyp |
hypothetical protein | 576 | 54 | textmining:571 |
Rv2081c |
transmembrane protein | 631 | 52 | textmining:627 |
Rv2660c hyp |
hypothetical protein | 562 | 50 | textmining:558 |
Rv1734c hyp |
hypothetical protein | 658 | 47 | textmining:656 |
Rv0061c hyp |
hypothetical protein | 651 | 41 | textmining:651 |
Rv1954A |
Rv1954A, len: 100 aa. Hypothetical unknown protein. | 513 | 41 | textmining:513 |
Rv1806 PE20 |
PE family protein PE20 | 433 | 41 | textmining:433 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: hypothetical protein
- MTBC0 PGAP product: hypothetical protein
- Foldseek best: 7x75-assembly1_D Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open (prob 0.04, E=8e+00, TM=0.33)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_215890.2)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt P71802 (TrEMBL, unreviewed; Predicted)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Model confidence: ESMFold per-residue pLDDT (mean 55.4, low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 11 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001475|Rv1374c| MVTSVADENVASRIASWGTGPAPDPRLDYAHAHLKGRRGRSPARPNAPIGARSFAVGRKICRVERFTLLEHGFVGHALHRVPCAGLVALVMSACSLAVCREVGNYAQRRVGRFAFFEQTFVRHALTPRCSRTDSKASYTQLNRICKFPPHWV