Rv2472 Still unknown · low auto-curated
H37Rv Rv2472 · MTBC0 mtbc0_002634 ·
97 aa · 2799520–2799813 (+) ·
RefSeq NP_216988.1
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: 7n51-assembly1_A Structure of a bacterial gasdermin from Vitiosangium (prob 0.03, TM 0.46). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53199
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 38.2 (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 |
|---|---|---|---|---|
7n51-assembly1_A |
0.03 | 0.46 | 4.8e+00 | 7n51-assembly1_A Structure of a bacterial gasdermin from Vitiosangium sp. |
1fg9-assembly1_E |
0.03 | 0.33 | 3.4e+00 | 1fg9-assembly1_E 3:1 COMPLEX OF INTERFERON-GAMMA RECEPTOR WITH INTERFERON-GAMMA DIMER |
8bfp-assembly1_M |
0.02 | 0.39 | 3.2e+00 | 8bfp-assembly1_M Jumbo Phage phi-kp24 empty capsid pentamer hexamers |
1oqj-assembly2_B |
0.01 | 0.26 | 8.2e+00 | 1oqj-assembly2_B Crystal structure of the SAND domain from glucocorticoid modulatory element binding protein-1 (GMEB1) |
6id9-assembly1_A |
0.01 | 0.41 | 9.4e+00 | 6id9-assembly1_A Crystal structure of H7 hemagglutinin mutant H7-SGTL ( A138S, V186G, P221T) from the influenza virus A/Anhui/1/2013 (H7N9) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: aglA (alpha-glucosidase AglA), medium confidence from genomic context alone (score 693 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) |
|---|---|---|---|---|
Rv2473 hyp |
hypothetical protein | 786 | 786 ctx | neighborhood:781 |
Rv1959c parE1 |
toxin ParE1 | 775 | 766 | experimental:756 |
Rv2471 aglA |
alpha-glucosidase AglA | 692 | 693 ctx | neighborhood:691 |
Rv2470 glbO |
hemoglobin GlbO | 638 | 639 ctx | neighborhood:637 |
Rv2469c hyp |
hypothetical protein | 457 | 458 ctx | neighborhood:451 |
Rv1102c mazF3 |
mRNA interferase MazF3 | 414 | 406 |
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: 7n51-assembly1_A Structure of a bacterial gasdermin from Vitiosangium sp. (prob 0.03, E=5e+00, TM=0.46)
- (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_216988.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt O53199 (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 38.2, very low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
6 functional partner(s); context anchor
aglA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002634|Rv2472| MMMRIAVRLPGEVITFVDSEVSQIRIPSRRAAVVLRASNASDAAILTATEPNHHLDALAGQAAKLAPTSIDAAHPARPARRDPCLYPRTGQALPRTG