Rv1706A Still unknown · low auto-curated
H37Rv Rv1706A · MTBC0 - ·
55 aa · 1934482–1934649 (-) ·
RefSeq YP_177651.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 3q1p-assembly1_B Crystal structure of CDP-Chase (prob 0.41, TM 0.85). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
Q79FL4
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 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 72.1 (confident). A confident model makes the fold comparison meaningful.
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 |
|---|---|---|---|---|
3q1p-assembly1_B |
0.41 | 0.85 | 5.3e+00 | 3q1p-assembly1_B Crystal structure of CDP-Chase |
5jbr-assembly1_B |
0.35 | 0.78 | 4.7e+00 | 5jbr-assembly1_B Crystal structure of uncharacterized protein Bcav_2135 from Beutenbergia cavernae |
6nci-assembly1_B |
0.33 | 0.86 | 6.6e+00 | 6nci-assembly1_B Crystal structure of CDP-Chase: Vector data collection |
1ezj-assembly1_A |
0.28 | 0.75 | 6.1e+00 | 1ezj-assembly1_A CRYSTAL STRUCTURE OF THE MULTIMERIZATION DOMAIN OF THE PHOSPHOPROTEIN FROM SENDAI VIRUS |
5n5f-assembly1_B |
0.18 | 0.74 | 9.9e+00 | 5n5f-assembly1_B Crystal structure of Haliangium ochraceum encapsulated ferritin |
6sv1-assembly1_F |
0.14 | 0.52 | 5.7e+00 | 6sv1-assembly1_F Crystal structure of Rhodospirillum rubrum Rru_A0973 E34A variant |
7s5c-assembly1_J |
0.13 | 0.66 | 9.9e+00 | 7s5c-assembly1_J M. xanthus ferritin-like protein EncB |
6suw-assembly3_V |
0.11 | 0.52 | 8.1e+00 | 6suw-assembly3_V Crystal structure of Rhodospirillum rubrum Rru_A0973 E31A variant |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1707 (transmembrane protein), medium confidence from genomic context alone (score 503 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) |
|---|---|---|---|---|
Rv1707 |
transmembrane protein | 503 | 503 ctx | neighborhood:498 |
Rv1710 scpB |
segregation and condensation protein ScpB | 460 | 459 ctx | neighborhood:459 |
Rv1708 |
initiation inhibitor protein | 460 | 459 ctx | neighborhood:459 |
Rv1713 engA |
GTPase Der | 453 | 453 ctx | neighborhood:452 |
Rv1712 cmk |
cytidylate kinase | 453 | 453 ctx | neighborhood:452 |
Rv1709 scpA |
segregation and condensation protein ScpA | 452 | 452 ctx | neighborhood:452 |
Rv1711 |
RNA pseudouridine synthase | 452 | 452 ctx | neighborhood:452 |
Rv1706c PPE23 |
PPE family protein PPE23 | 871 | 50 | textmining:870 |
Rv3047c hyp |
hypothetical protein | 804 | 47 | textmining:803 |
Rv0190 ricR hyp |
hypothetical protein | 436 | 47 | textmining:433 |
Rv2325c hyp |
hypothetical protein | 803 | 45 | textmining:803 |
Rv1382 hyp |
hypothetical protein | 658 | 43 | textmining:658 |
Rv2898c hyp |
hypothetical protein | 803 | 41 | textmining:803 |
Rv3102c ftsE |
cell division ATP-binding protein FtsE | 517 | 41 | textmining:517 |
Rv2736c recX |
regulatory protein RecX | 432 | 41 | textmining:432 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Foldseek best: 3q1p-assembly1_B Crystal structure of CDP-Chase (prob 0.41, E=5e+00, TM=0.85)
- (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 YP_177651.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt Q79FL4 (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 72.1, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
15 functional partner(s); context anchor
Rv1707 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1706A| MGSLAAFKLGWLLSAMAPNVVLLTAFRVPQGLTMLTVFATGQAGQHRCRTFHVTP