Rv0236A Still unknown · low auto-curated
H37Rv Rv0236A · MTBC0 - ·
57 aa · 286898–287071 (-) ·
RefSeq YP_177619.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF2613. 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 |
P9WLB1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative secreted protein Rv0236A |
UniProt still lists this protein as Putative secreted protein Rv0236A; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF2613) |
| Orthologous group | 2A0FU |
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, 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DUF2613 | PF11021.14 | 3.1e-22 | 3–56 | Protein of unknown function (DUF2613) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lpqI (lipoprotein LpqI), high confidence from genomic context alone (score 781 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) |
|---|---|---|---|---|
Rv0237 lpqI |
lipoprotein LpqI | 781 | 781 ctx | neighborhood:778 |
Rv0236c aftD |
alpha-(1->3)-arabinofuranosyltransferase | 729 | 729 ctx | neighborhood:728 |
Rv0235c |
transmembrane protein | 597 | 597 ctx | neighborhood:597 |
Rv0238 |
transcriptional regulator | 521 | 521 ctx | neighborhood:518 |
Rv0234c gabD1 |
succinate-semialdehyde dehydrogenase | 498 | 498 ctx | neighborhood:496 |
Rv2171 lppM |
lipoprotein LppM | 805 | 53 | textmining:803 |
Rv2172c hyp |
hypothetical protein | 806 | 47 | textmining:805 |
Rv1304 atpB |
ATP synthase subunit A | 544 | 47 | textmining:542 |
Rv0287 esxG |
ESAT-6 like protein EsxG | 413 | 47 | textmining:410 |
Rv3392c cmaA1 |
cyclopropane mycolic acid synthase CmaA | 631 | 46 | textmining:630 |
Rv3019c esxR |
ESAT-6 like protein EsxR | 512 | 44 | textmining:511 |
Rv0197 |
oxidoreductase | 654 | 41 | textmining:654 |
Rv3022c PPE48 |
Rv3021c, (MTV012.35c), len: 358 aa. PPE47, Member of Mycobacterium tuberculosis PPE family. Should be continuation of upstream ORF MTV012.36 | 510 | 41 | textmining:510 |
Rv0285 PE5 |
PE family protein PE5 | 481 | 41 | textmining:481 |
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): DUF2613 PF11021.14 (E=3e-22)
- (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_177619.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF2613 (PF11021.14)
- 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
2A0FU - Curated reference: UniProt P9WLB1 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 62.4, low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
14 functional partner(s); context anchor
lpqI - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0236A| MNRIVAPAAASVVVGLLLGAAAIFGVTLMVQQDKKPPLPGGDPSSSVLNRVEYGNRS