Rv3032A Family assigned · low
H37Rv Rv3032A · MTBC0 - ·
129 aa · 3392812–3393201 (+) ·
RefSeq YP_004837058.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Membrane metalloprotease-like fold (YxkI-like). RefSeq leaves it 'hypothetical protein'. |
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 |
I6X630
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 | 2C72U |
|---|
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 0 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 70.3 (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 |
|---|---|---|---|---|
4khb-assembly4_G |
0.63 | 0.50 | 4.0e-01 | 4khb-assembly4_G Structure of the Spt16D Pob3N heterodimer |
4khb-assembly1_A |
0.51 | 0.49 | 4.2e-01 | 4khb-assembly1_A Structure of the Spt16D Pob3N heterodimer |
4khb-assembly3_E |
0.41 | 0.50 | 6.2e-01 | 4khb-assembly3_E Structure of the Spt16D Pob3N heterodimer |
4khb-assembly2_C |
0.38 | 0.47 | 5.0e-01 | 4khb-assembly2_C Structure of the Spt16D Pob3N heterodimer |
2gcl-assembly2_B |
0.18 | 0.57 | 3.9e+00 | 2gcl-assembly2_B Structure of the Pob3 Middle domain |
4tyz-assembly2_B |
0.15 | 0.47 | 2.3e+00 | 4tyz-assembly2_B Crystal structure of the C-terminal domain of an unknown protein from Leishmania infantum |
8xgc-assembly1_M |
0.11 | 0.36 | 1.2e+00 | 8xgc-assembly1_M Structure of yeast replisome associated with FACT and histone hexamer, Composite map |
3to1-assembly1_A |
0.07 | 0.47 | 7.3e+00 | 3to1-assembly1_A Two surfaces on Rtt106 mediate histone binding and chaperone activity |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3032 (glycogen synthase), high confidence from genomic context alone (score 752 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) |
|---|---|---|---|---|
Rv3032 |
glycogen synthase | 752 | 752 ctx | neighborhood:752 |
Rv3030 |
S-adenosylmethionine-dependent methyltransferase | 585 | 585 ctx | neighborhood:585 |
Rv3031 |
1,4-alpha-glucan-branching protein | 585 | 585 ctx | neighborhood:585 |
Rv3033 hyp |
hypothetical protein | 485 | 485 ctx | neighborhood:485 |
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
- Foldseek vs AFDB-SwissProt: membrane metalloprotease YxkI, TM 0.63, E 4e-3
- Structural homology vs AlphaFold-Swiss-Prot (Foldseek; 542k curated SwissProt structures), project 'Still unknown gene function' phase13, 2026-06-10. Fold/family-level, not a demonstrated function.
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_004837058.1)
- 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
2C72U - Curated reference: UniProt I6X630 (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 70.3, confident)
- 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
Rv3032 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3032A| MKPQDQGLHFPYRYDLRLAPMWLPFRWPGSQGVTVTEDGRFVARYGPFRVEAPLSSVRDAHITGPYRWWTAVGPRLSMVDDGLTFGTNAAAGVCIHFEPRIHRVIGLRDHSALTVTVADPEGLVAALSS