Rv3047c Still unknown · low auto-curated
H37Rv Rv3047c · MTBC0 mtbc0_003239 ·
94 aa · 3429332–3429616 (-) ·
RefSeq NP_217563.1
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: 5y5z-assembly1_Y V/A-type ATPase/synthase from Thermus thermophilus, r (prob 0.06, TM 0.40). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X642
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) pseudogene candidate
| pN/pS | 0.676 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 2.25% of strains (3265) · 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 42.1 (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 |
|---|---|---|---|---|
5y5z-assembly1_Y |
0.06 | 0.40 | 6.2e+00 | 5y5z-assembly1_Y V/A-type ATPase/synthase from Thermus thermophilus, rotational state 2 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nrdF2 (ribonucleoside-diphosphate reductase subunit beta NrdF2), high confidence from genomic context alone (score 935 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) |
|---|---|---|---|---|
Rv3048c nrdF2 |
ribonucleoside-diphosphate reductase subunit beta NrdF2 | 935 | 935 ctx | neighborhood:578 coexpression:853 |
Rv3046c hyp |
hypothetical protein | 416 | 416 ctx | neighborhood:416 |
Rv2736c recX |
regulatory protein RecX | 518 | 55 | textmining:511 |
Rv2898c hyp |
hypothetical protein | 809 | 47 | textmining:808 |
Rv1706A hyp |
hypothetical protein | 804 | 47 | textmining:803 |
Rv1706c PPE23 |
PPE family protein PPE23 | 659 | 46 | textmining:658 |
Rv2325c hyp |
hypothetical protein | 808 | 44 | textmining:808 |
Rv3102c ftsE |
cell division ATP-binding protein FtsE | 651 | 44 | textmining:650 |
Rv1382 hyp |
hypothetical protein | 803 | 41 | textmining:803 |
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: 5y5z-assembly1_Y V/A-type ATPase/synthase from Thermus thermophilus, rotational (prob 0.06, E=6e+00, TM=0.40)
- (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_217563.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt I6X642 (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 42.1, very low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
9 functional partner(s); context anchor
nrdF2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003239|Rv3047c| MGGPFDADAEAHFDEVAEAFAKLTNVDRDVGVDLEKELCMTVEADDRSDALVTRRLLPRVPRCIPLAARLAPGTIGCPSFWNPIATGGASRQAL