Rv3098c Still unknown · low auto-curated
H37Rv Rv3098c · MTBC0 mtbc0_003292 ·
150 aa · 3488574–3489026 (-) ·
RefSeq NP_217614.1
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: 6xr2-assembly2_E Computationally designed right-handed alpha/alpha hom (prob 0.66, TM 0.57). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05776
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 | 0.367 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.26% of strains (374) · 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 51.2 (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 |
|---|---|---|---|---|
6xr2-assembly2_E |
0.66 | 0.57 | 1.4e+00 | 6xr2-assembly2_E Computationally designed right-handed alpha/alpha homotrimeric toroid with 3 repeats per subunit |
6xr2-assembly1_B |
0.57 | 0.54 | 1.8e+00 | 6xr2-assembly1_B Computationally designed right-handed alpha/alpha homotrimeric toroid with 3 repeats per subunit |
6xr2-assembly1_C |
0.57 | 0.48 | 1.1e+00 | 6xr2-assembly1_C Computationally designed right-handed alpha/alpha homotrimeric toroid with 3 repeats per subunit |
3f4m-assembly1_A |
0.35 | 0.38 | 8.4e-01 | 3f4m-assembly1_A Crystal structure of TIPE2 |
6xr2-assembly2_F |
0.33 | 0.46 | 2.2e+00 | 6xr2-assembly2_F Computationally designed right-handed alpha/alpha homotrimeric toroid with 3 repeats per subunit |
8e0n-assembly1_A |
0.33 | 0.53 | 3.6e+00 | 8e0n-assembly1_A Homotrimeric variant of tcTRP9, BGL18 |
8e0o-assembly1_C |
0.25 | 0.53 | 4.2e+00 | 8e0o-assembly1_C Heterotrimeric variant of tcTRP9, hetBGL03-15-18 |
6e9t-assembly1_B |
0.21 | 0.49 | 4.4e+00 | 6e9t-assembly1_B DHF58 filament |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3098A (PemK-like protein), medium confidence from genomic context alone (score 572 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) |
|---|---|---|---|---|
Rv3098A |
PemK-like protein | 572 | 572 ctx | neighborhood:572 |
Rv3097c lipY |
triacylglycerol lipase Lip | 506 | 506 ctx | neighborhood:506 |
Rv3100c smpB |
SsrA-binding protein | 870 | 47 | textmining:870 |
Rv3102c ftsE |
cell division ATP-binding protein FtsE | 870 | 44 | textmining:870 |
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: 6xr2-assembly2_E Computationally designed right-handed alpha/alpha homotrimeric (prob 0.66, E=1e+00, TM=0.57)
- (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_217614.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt O05776 (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 51.2, low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
4 functional partner(s); context anchor
Rv3098A - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003292|Rv3098c| MASLRIAEVDPVDRSPNHHASGSVETSSSRSRSASVRACLIHTSRSSSCSARRMTSLLRSPLRIAALMICSSFSVGRKPMVAVMSTTIADVAQSYSNCSTHSGTPTPAFAASFLLDAINAPRVIAGRFASESVRFPAAAPHGSVPSRLPV