aprA Resolved · medium auto-curated
H37Rv Rv2395A · MTBC0 - ·
71 aa · 2692224–2692439 (+) ·
RefSeq YP_007411091.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acid and phagosome regulated protein AprA |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Acid and phagosome regulated protein AprA. |
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 |
V5QPR9
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Acid and phagosome regulated protein A AprA |
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.364 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.10% of strains (152) · clonal |
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).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: aprB (acid and phagosome regulated protein AprB), medium confidence from genomic context alone (score 511 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2395B aprB |
acid and phagosome regulated protein AprB | 822 | 511 ctx | neighborhood:511 textmining:651 |
Rv2395 |
integral membrane protein | 599 | 476 ctx | neighborhood:476 |
Rv2396 PE_PGRS41 |
acid and phagosome regulated protein AprC | 565 | 378 | |
Rv3309c upp |
uracil phosphoribosyltransferase | 629 | 41 | textmining:629 |
Rv3208 |
TetR family transcriptional regulator | 511 | 41 | textmining:511 |
Rv2093c tatC |
Sec-independent protein translocase transmembrane protein TatC | 435 | 41 | 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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): acid and phagosome regulated protein AprA
- (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_007411091.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt V5QPR9 (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)
- 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
aprB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2395A|aprA MTMTASVAKVTAARPEPSAAWAEARRRVRQRREDMLRHPAFLSKQLPAEPADDDGVAAVYDIAIARRRRPA