PE_PGRS47 Family assigned · medium auto-curated
H37Rv Rv2741 · MTBC0 - ·
525 aa · 3053914–3055491 (+) ·
RefSeq YP_177902.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PE-PGRS family protein PE_PGRS47 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PE-PGRS family protein PE_PGRS47. Pfam: PE (PF00934.26), PGRS (PF21526.3). |
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 |
Q79FB3
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | PE-PGRS family protein PE_PGRS47 |
| Curated function | Contributes to evasion of both innate and adaptive immunity. Inhibits autophagy in infected host phagocytes and inhibits major histocompatibility complex (MHC) class II antigen presentation by mycobacteria-infected dendritic cells. Has an important role in the growth and survival of M.tuberculosis, particularly during intracellular growth and in the later chronic phase of infection. |
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 | 0.317 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 11.57% of strains (16802) · 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 | 1.5e-32 | 4–94 | PE family |
PGRS | PF21526.3 | 1.5e-07 | 118–189 | PGRS repeats |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ephG (epoxide hydrolase), medium confidence from genomic context alone (score 461 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2740 ephG |
epoxide hydrolase | 461 | 461 ctx | neighborhood:461 |
Rv2352c PPE38 |
PPE family protein PPE38 | 625 | 41 | textmining:625 |
Rv0388c PPE9 |
Rv0388c, (MTV036.23c), len: 180 aa. PPE9, Member of the Mycobacterium tuberculosis PPE family, highly similar to others e.g. MTCY10G2_10|Z92 | 485 | 41 | textmining:485 |
Rv0878c PPE13 |
PPE family protein PPE13 | 438 | 41 | textmining:438 |
Rv3892c PPE69 |
PPE family protein PPE69 | 431 | 41 | textmining:431 |
Rv2544 lppB |
lipoprotein LppB | 403 | 41 | textmining:403 |
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): PE-PGRS family protein PE_PGRS47
- Pfam (hmmscan --cut_ga): PE PF00934.26 (E=2e-32), PGRS PF21526.3 (E=1e-07)
- (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_177902.1)
- Domains: Pfam-A via hmmscan --cut_ga — PE (PF00934.26), PGRS (PF21526.3)
- 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 Q79FB3 (SwissProt, reviewed; Inferred from homology)
- 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
ephG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2741|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