Rv1366A Still unknown · low auto-curated
H37Rv Rv1366A · MTBC0 - ·
86 aa · 1539180–1539440 (+) ·
RefSeq YP_004837053.2
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: 9erv-assembly1_A Structure of Salmonella CapRel bound to Bas11 Gp54 (prob 0.30, TM 0.40). |
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 |
V5QQR7
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2DS19 |
|---|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.318 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 74.0 (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 |
|---|---|---|---|---|
9erv-assembly1_A |
0.30 | 0.40 | 2.8e-01 | 9erv-assembly1_A Structure of Salmonella CapRel bound to Bas11 Gp54 |
7x39-assembly1_A |
0.12 | 0.48 | 2.2e+00 | 7x39-assembly1_A Structure of CIZ1 bound ERH |
7ohx-assembly1_H |
0.11 | 0.51 | 2.6e+00 | 7ohx-assembly1_H Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A |
3egr-assembly1_B-2 |
0.10 | 0.44 | 3.0e+00 | 3egr-assembly1_B-2 CRYSTAL STRUCTURE OF A PHENYLACETATE-COA OXYGENASE SUBUNIT PAAB (REUT_A2307) FROM RALSTONIA EUTROPHA JMP134 AT 2.65 A RESOLUTION |
1ln0-assembly1_A |
0.09 | 0.39 | 3.4e+00 | 1ln0-assembly1_A Structure of the Catalytic Domain of Homing Endonuclease I-TevI |
4zfj-assembly3_I |
0.07 | 0.46 | 4.2e+00 | 4zfj-assembly3_I Ergothioneine-biosynthetic Ntn hydrolase EgtC, apo form |
4zfk-assembly1_A |
0.06 | 0.46 | 6.2e+00 | 4zfk-assembly1_A Ergothioneine-biosynthetic Ntn hydrolase EgtC with glutamine |
1mk0-assembly1_A |
0.04 | 0.38 | 8.6e+00 | 1mk0-assembly1_A catalytic domain of intron endonuclease I-TevI, E75A mutant |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rsfA (anti-sigma-F factor antagonist RsfA), medium confidence from genomic context alone (score 496 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) |
|---|---|---|---|---|
Rv1366 hyp |
hypothetical protein | 834 | 834 ctx | neighborhood:834 |
Rv1365c rsfA |
anti-sigma-F factor antagonist RsfA | 495 | 496 ctx | neighborhood:496 |
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: 9erv-assembly1_A Structure of Salmonella CapRel bound to Bas11 Gp54 (prob 0.30, E=3e-01, 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 YP_004837053.2)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
2DS19 - Curated reference: UniProt V5QQR7 (TrEMBL, unreviewed; Evidence at protein 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 74.0, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
2 functional partner(s); context anchor
rsfA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1366A| MRPSRQGEVGEVAGYVVEYNRRTHVRRITEFATPQEAMEHRLKLEAERTDSNIEIVALVSKSLGTLKQTHSRYFTGEELNVGNGAR