PE_PGRS41 Resolved · high auto-curated
H37Rv Rv2396 · MTBC0 - ·
361 aa · 2692799–2693884 (+) ·
RefSeq YP_177878.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acid and phagosome regulated protein AprC |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Acid and phagosome regulated protein AprC. Pfam: PE (PF00934.26). |
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 |
Q79FE6
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | PE-PGRS family protein PE_PGRS41 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | PE-PGRS family |
| Orthologous group | COG3391 |
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) pseudogene candidate
| pN/pS | 0.793 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 8 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 1.91% of strains (2778) · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
PE | PF00934.26 | 2.8e-33 | 4–94 | PE family |
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 556 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2395B aprB |
acid and phagosome regulated protein AprB | 775 | 556 ctx | neighborhood:556 textmining:513 |
Rv0198c zmp1 |
zinc metalloprotease | 495 | 407 | |
Rv2395A aprA |
acid and phagosome regulated protein AprA | 565 | 378 | |
Rv2395 |
integral membrane protein | 850 | 265 | textmining:805 |
Rv2633c hyp |
hypothetical protein | 466 | 95 | textmining:435 |
Rv2093c tatC |
Sec-independent protein translocase transmembrane protein TatC | 449 | 55 | textmining:441 |
Rv1004c |
membrane protein | 439 | 43 | textmining:438 |
Rv0453 PPE11 |
PPE family protein PPE11 | 439 | 41 | textmining:439 |
Rv3289c |
transmembrane protein | 438 | 41 | textmining:438 |
Rv0757 phoP |
two component system response transcriptional positive regulator PhoP | 436 | 41 | textmining:436 |
Rv0047c hyp |
hypothetical protein | 436 | 41 | textmining:436 |
Rv3746c PE34 |
PE family protein PE34 | 434 | 41 | textmining:434 |
Rv2629 hyp |
hypothetical protein | 431 | 41 | textmining:431 |
Rv0822c hyp |
hypothetical protein | 431 | 41 | textmining:431 |
Rv2632c hyp |
hypothetical protein | 430 | 41 | textmining:430 |
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 AprC
- Pfam (hmmscan --cut_ga): PE PF00934.26 (E=3e-33)
- (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_177878.1)
- Domains: Pfam-A via hmmscan --cut_ga — PE (PF00934.26)
- 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
COG3391 - Curated reference: UniProt Q79FE6 (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 —
16 functional partner(s); context anchor
aprB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2396|PE_PGRS41 MSFLIASPEALAATATYLTGIGSAISAANAVAAAPTTEILAAGTDEVSTAISALFGAHAQAYQALSAHVAAFHDQFVHTLTAGAGSYMAAEAAAASPLQALQLELLNAINAPTLALLGRPLIGDGTDAAPGSGGAGGAGGILIGNGGTGGASDLAGTGRGGVGGAGGAGGLFGIGGAGGGCGSAVAIGGDGGAGGAGGVFSGGGAGGAGDAIGGSGGAGGTGGLLGGGGGAGGAGGAGGNGGGASNSASIGGDGGSGGAGGMLYGAGGVGGNGGAAVAIGGDGGAGGRAGAIGNGGDGGNGGTSNTPGGSGGDGGNGGNAGLIGNGGNGGNAEIVISGGSVAGTGGNGGLLLGFNGTNGLP