Rv0026 Still unknown · low auto-curated
H37Rv Rv0026 · MTBC0 - ·
448 aa · 29722–31068 (+) ·
RefSeq NP_214540.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF4226. Function unknown. |
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 |
P9WMB1
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv0026 |
UniProt still lists this protein as Uncharacterized protein Rv0026; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Domain of unknown function (DUF4226) |
| Orthologous group | 2ATF1 |
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 | 0.939 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 13 missense, 0 nonsense, 4 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 27.83% of strains (40408) · convergent |
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 |
|---|---|---|---|---|
DUF4226 | PF10774.16 | 1.5e-38 | 76–188 | Domain of unknown function (DUF4226) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0023 (transcriptional regulator), medium confidence from genomic context alone (score 512 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) |
|---|---|---|---|---|
Rv0025 hyp |
hypothetical protein | 641 | 641 ctx | neighborhood:638 |
Rv0027 hyp |
hypothetical protein | 536 | 536 ctx | neighborhood:529 |
Rv0028 hyp |
hypothetical protein | 535 | 534 ctx | neighborhood:528 |
Rv0023 |
transcriptional regulator | 511 | 512 ctx | neighborhood:507 |
Rv0024 |
NLP/P60 family protein | 446 | 446 ctx | neighborhood:438 |
Rv0022c whiB5 |
transcriptional regulator WhiB5 | 418 | 382 | |
Rv0570 nrdZ |
vitamin B12-dependent ribonucleoside-diphosphate reductase | 532 | 85 | textmining:510 |
Rv0938 ligD |
multifunctional non-homologous end joining DNA repair protein/ATP dependent DNA ligase LigD | 520 | 54 | textmining:514 |
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
- Pfam (hmmscan --cut_ga): DUF4226 PF10774.16 (E=1e-38)
- (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_214540.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF4226 (PF10774.16)
- 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
2ATF1 - Curated reference: UniProt P9WMB1 (SwissProt, reviewed; 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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
8 functional partner(s); context anchor
Rv0023 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0026| MAFDAAMSTHEDLLATIRYVRDRTGDPNAWQTGLTPTEVTAVVTSTTRSEQLDAILRKIRQRHSNLYYPAPPDREQGDAARAIADAEAALAHQNSATAQLDLQVVSAILNAHLKTVEGGESLHELQQEIEAAVRIRSDLDTPAGARDFQRFLIGKLKDIREVVATASLDAASKSALMAAWTSLYDASKGDRGDADDRGPASVGSGGAPARGAGQQPELPTRAEPDCLLDSLLLEDPGLLADDLQVPGGTSAAIPSASSTPSLPNLGGATMPGGGATPALVPGVSAPGGLPLSGLLRGVGDEPELTDFDERGQEVRDPADYEHSNEPDERRADDREGADEDAGLGKSESPPQAPTTVTLPNGETVTAASPQLAAAIKAAASGTPIADAFQQQGIAIPLPGTAVANPVDPARISAGDVGVFTATPLPLALAKLFWTARFNTSQPCEGQTF