Rv2240c Family assigned · medium auto-curated
H37Rv Rv2240c · MTBC0 mtbc0_002382 ·
196 aa · 2537848–2538438 (-) ·
RefSeq NP_216756.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Contains Rv2240c (PF27150.1) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLG7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2240c |
UniProt still lists this protein as Uncharacterized protein Rv2240c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2AP8W |
|---|---|
| Gene Ontology (2) |
GO:0005575, GO:0005576
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 3 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Rv2240c | PF27150.1 | 2.0e-40 | 73–192 | Rv2240c four-helix bundle domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ahpE (peroxiredoxin), high confidence from genomic context alone (score 836 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) |
|---|---|---|---|---|
Rv2238c ahpE |
peroxiredoxin | 927 | 836 ctx | neighborhood:829 textmining:573 |
Rv2239c hyp |
hypothetical protein | 977 | 831 ctx | neighborhood:829 textmining:870 |
Rv2241 aceE |
pyruvate dehydrogenase E1 component | 740 | 740 ctx | neighborhood:736 |
Rv2242 hyp |
hypothetical protein | 452 | 451 ctx | neighborhood:448 |
Rv2237A hyp |
hypothetical protein | 430 | 430 ctx | neighborhood:430 |
Rv0497 |
transmembrane protein | 451 | 70 | textmining:434 |
Rv2439c proB |
glutamate 5-kinase protein | 517 | 53 | textmining:511 |
Rv2441c rpmA |
50S ribosomal protein L27 | 549 | 52 | textmining:544 |
Rv2440c obg |
GTPase Obg | 804 | 50 | textmining:803 |
Rv1365c rsfA |
anti-sigma-F factor antagonist RsfA | 722 | 47 | textmining:721 |
Rv2638 hyp |
hypothetical protein | 519 | 47 | textmining:516 |
Rv3604c |
transmembrane protein | 437 | 47 | textmining:434 |
Rv1904 hyp |
hypothetical protein | 519 | 46 | textmining:517 |
Rv3287c rsbW |
anti-sigma factor RsbW | 631 | 45 | textmining:630 |
Rv0516c oprA |
anti-anti-sigma factor | 437 | 45 | textmining:435 |
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
- Pfam (hmmscan --cut_ga): Rv2240c PF27150.1 (E=2e-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_216756.2)
- Domains: Pfam-A via hmmscan --cut_ga — Rv2240c (PF27150.1)
- 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
2AP8W - Curated reference: UniProt P9WLG7 (SwissProt, reviewed; 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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
19 functional partner(s); context anchor
ahpE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002382|Rv2240c| MLIGWRAVPRRHGGELPRRGALALGCIALLLMGIVGCTTVTDGTAMPDTNVAPAYRSSVSASVSASAATSSIRESQRQQSLTTKAIRTSCDALAATSKDAIDKVNAYVAAFNQGRNTGPTEGPAIDALNNSASTVSGSLSAALSAQLGDALNAYVDAARAVANAIGAHASTAEFNRRVDRLNDTKTKALKMCVAAF