Rv1954c Still unknown · low auto-curated
H37Rv Rv1954c · MTBC0 mtbc0_002069 ·
173 aa · 2220339–2220860 (-) ·
RefSeq NP_216470.1
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: 3g02-assembly1_A Structure of enantioselective mutant of epoxide hydro (prob 0.04, TM 0.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLQ3
SwissProt · reviewed
· Evidence at transcript level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1954c |
UniProt still lists this protein as Uncharacterized protein Rv1954c; the revised annotation above is ahead of the current UniProt record.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.501 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 missense, 0 nonsense, 0 frameshift |
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 39.3 (very 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 |
|---|---|---|---|---|
3g02-assembly1_A |
0.04 | 0.24 | 1.1e+00 | 3g02-assembly1_A Structure of enantioselective mutant of epoxide hydrolase from Aspergillus niger generated by directed evolution |
3g02-assembly1_B |
0.04 | 0.24 | 1.4e+00 | 3g02-assembly1_B Structure of enantioselective mutant of epoxide hydrolase from Aspergillus niger generated by directed evolution |
1qo7-assembly1_A |
0.03 | 0.25 | 1.6e+00 | 1qo7-assembly1_A Structure of Aspergillus niger epoxide hydrolase |
6n04-assembly1_A |
0.02 | 0.38 | 8.1e+00 | 6n04-assembly1_A The X-ray crystal structure of AbsH3, an FAD dependent reductase from the Abyssomicin biosynthesis pathway in Streptomyces |
5nff-assembly12_L |
0.01 | 0.20 | 3.6e+00 | 5nff-assembly12_L Crystal structure of GP1 receptor binding domain from Morogoro virus |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2660c hyp |
hypothetical protein | 641 | 70 | textmining:630 |
Rv1955 higB |
toxin HigB | 527 | 70 | textmining:513 |
Rv1374c hyp |
hypothetical protein | 521 | 55 | textmining:514 |
Rv1957 secBL |
SecB-like chaperone | 524 | 52 | textmining:519 |
Rv3288c usfY hyp |
hypothetical protein | 633 | 49 | textmining:630 |
Rv0188 |
transmembrane protein | 483 | 47 | textmining:480 |
Rv3661 hyp |
hypothetical protein | 441 | 42 | textmining:441 |
Rv0061c hyp |
hypothetical protein | 652 | 41 | textmining:652 |
Rv1954A |
Rv1954A, len: 100 aa. Hypothetical unknown protein. | 540 | 41 | textmining:540 |
Rv3182 higB3 hyp |
hypothetical protein | 410 | 41 | textmining:410 |
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: 3g02-assembly1_A Structure of enantioselective mutant of epoxide hydrolase from (prob 0.04, E=1e+00, TM=0.24)
- (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_216470.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt P9WLQ3 (SwissProt, reviewed; Evidence at transcript level)
- 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 39.3, very low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 10 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002069|Rv1954c| MAAGSGGGTVGLVLPRVASLSGLDGAPTVPEGSDKALMHLGDPPRRCDTHPDGTSSAAAALVLRRIDVHPLLTGLGRGRQTVSLRNGHLVATANRAILSRRRSRLTRGRSFTSHLITSCPRLDDHQHRHPTRCRAEHAGCTVATCIPNAHDPAPGHQTPRWGPFRLKPAYTRI