Rv0942 Still unknown · low auto-curated
H37Rv Rv0942 · MTBC0 mtbc0_001000 ·
92 aa · 1055577–1055855 (+) ·
RefSeq NP_215457.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF8092. Function unknown. Foldseek best (non-significant) hit: 7va4-assembly1_D Telomeric tetranucleosome in open state (prob 0.06, TM 0.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKN9
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv0942 |
UniProt still lists this protein as Uncharacterized protein Rv0942; the revised annotation above is ahead of the current UniProt record.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 1.011 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DUF8092 | PF26357.1 | 1.8e-40 | 10–63 | Domain of unknown function (DUF8092) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 38.8 (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 |
|---|---|---|---|---|
7va4-assembly1_D |
0.06 | 0.28 | 2.8e+00 | 7va4-assembly1_D Telomeric tetranucleosome in open state |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0940c (oxidoreductase), medium confidence from genomic context alone (score 416 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0941c hyp |
hypothetical protein | 572 | 572 ctx | neighborhood:571 |
Rv0940c |
oxidoreductase | 417 | 416 ctx | neighborhood:414 |
Rv0886 fprB |
ferredoxin/ferredoxin--NADP reductase | 543 | 47 | textmining:541 |
Rv0887c hyp |
hypothetical protein | 808 | 44 | textmining:808 |
Rv0911 hyp |
hypothetical protein | 804 | 44 | textmining:804 |
Rv1731 gabD2 |
succinate-semialdehyde dehydrogenase | 657 | 44 | textmining:656 |
Rv0912 |
transmembrane protein | 809 | 42 | textmining:809 |
Rv0234c gabD1 |
succinate-semialdehyde dehydrogenase | 801 | 42 | textmining:801 |
Rv0181c hyp |
hypothetical protein | 810 | 41 | textmining:810 |
Rv0180c |
transmembrane protein | 752 | 41 | textmining:752 |
Rv2009 vapB15 |
antitoxin VapB15 | 656 | 41 | textmining:656 |
Rv0183 |
lysophospholipase | 654 | 41 | textmining:654 |
Rv2010 vapC15 |
ribonuclease VapC15 | 640 | 41 | textmining:640 |
Rv0654 |
carotenoid cleavage oxygenase | 511 | 41 | textmining:511 |
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
- Pfam (hmmscan --cut_ga): DUF8092 PF26357.1 (E=2e-40)
- Foldseek best: 7va4-assembly1_D Telomeric tetranucleosome in open state (prob 0.06, E=3e+00, TM=0.28)
- (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_215457.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF8092 (PF26357.1)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt P9WKN9 (SwissProt, reviewed; 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 38.8, very low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
14 functional partner(s); context anchor
Rv0940c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001000|Rv0942| MGRSATIAMVPKRRDAMNRHSGPILSSGFIASSSNSCPANSLRMPSALAAETLSFDDRAVRRSTHHPGGGYPQKHAINLQSGLCPAYANASR