PE_PGRS4 Family assigned · medium auto-curated
H37Rv Rv0279c · MTBC0 - ·
837 aa · 336560–339073 (-) ·
RefSeq YP_177708.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PE-PGRS family protein PE_PGRS4 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PE-PGRS family protein PE_PGRS4. 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 |
L0T4W6
SwissProt · reviewed
· Evidence at transcript level
|
|---|---|
| UniProt name | PE-PGRS family protein PE_PGRS4 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| eggNOG description | acetylesterase activity |
| Orthologous group | COG0657 |
| EC number |
EC 3.1.1.3
|
| KEGG orthology |
K01046
|
| KEGG pathways |
map00561, map01100
|
| KEGG modules |
M00098
|
| Gene Ontology (54) |
GO:0003674, GO:0003824, GO:0004806, GO:0005488, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006950, GO:0008150, GO:0009405, GO:0009605 +42 more
|
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 | 0.523 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 18 synonymous, 23 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.15% of strains (220) · 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 | 1.8e-32 | 4–94 | PE family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PE_PGRS3 (PE-PGRS family protein PE_PGRS3), medium confidence from genomic context alone (score 423 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0284 eccC3 |
ESX-3 secretion system protein EccC3 | 440 | 440 | |
Rv0278c PE_PGRS3 |
PE-PGRS family protein PE_PGRS3 | 430 | 423 ctx | neighborhood:423 |
Rv0280 PPE3 |
PPE family protein PPE3 | 413 | 413 ctx | neighborhood:413 |
Rv0198c zmp1 |
zinc metalloprotease | 407 | 407 | |
Rv0277A vapB25 |
Rv0277A, len: 85 aa. Possible vapB25, antitoxin,part of toxin-antitoxin (TA) operon with Rv0277c, see Arcus et al. 2005. Has in-frame stop c | 400 | 400 ctx | neighborhood:400 |
Rv3213c |
SOJ/ParA-like protein | 704 | 241 | textmining:627 |
Rv2813 hyp |
hypothetical protein | 520 | 59 | textmining:511 |
Rv3212 hyp |
hypothetical protein | 803 | 43 | textmining:803 |
Rv1175c fadH |
NADPH dependent 2,4-dienoyl-CoA reductase FadH | 512 | 43 | textmining:511 |
Rv2543 lppA |
lipoprotein LppA | 511 | 41 | textmining:511 |
Rv1705c PPE22 |
PPE family protein PPE22 | 511 | 41 | textmining:511 |
Rv2544 lppB |
lipoprotein LppB | 511 | 41 | textmining:511 |
Rv2178c aroG |
phospho-2-dehydro-3-deoxyheptonate aldolase AroG | 438 | 41 | textmining:438 |
Rv2126c PE_PGRS37 |
PE-PGRS family protein PE_PGRS37 | 436 | 41 | textmining:436 |
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_PGRS4
- Pfam (hmmscan --cut_ga): PE PF00934.26 (E=2e-32)
- (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_177708.1)
- 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
COG0657 - Curated reference: UniProt L0T4W6 (SwissProt, reviewed; Evidence at transcript 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)
- 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
PE_PGRS3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0279c|PE_PGRS4 MSFVIAAPEVIAAAATDLASLESSIAAANAAAAANTTALLAAGADEVSTAVAALFGAHGQAYQALSAQAQAFHAQFVQALTSGGGAYAAAEAAATSPLLAPINEFFLANTGRPLIGNGTNGAPGTGANGGDGGWLIGNGGAGGSGAAGVNGGAGGNGGAGGLIGNGGAGGAGGRASTGTGGAGGAGGAAGMLFGAAGVGGPGGFAAAFGATGGAGGAGGNGGLFADGGVGGAGGATDAGTGGAGGSGGNGGLFGAGGTGGPGGFGIFGGGAGGDGGSGGLFGAGGTGGSGGTSIINVGGNGGAGGDAGMLSLGAAGGAGGSGGSNPDGGGGAGGIGGDGGTLFGSGGAGGVCGLGFDAGGAGGAGGKAGLLIGAGGAGGAGGGSFAGAGGTGGAGGAPGLVGNAGNGGNGGASANGAGAAGGAGGSGVLIGNGGNGGSGGTGAPAGTAGAGGLGGQLLGRDGFNAPASTPLHTLQQQILNAINEPTQALTGRPLIGNGANGTPGTGADGGAGGWLFGNGGNGGHGATGADGGDGGSGGAGGILSGIGGTGGSGGIGTTGQGGTGGTGGAALLIGSGGTGGSGGFGLDTGGAGGRGGDAGLFLGAAGTGGQAALSQNFIGAGGTAGAGGTGGLFANGGAGGAGGFGANGGTGGNGLLFGAGGTGGAGTLGADGGAGGHGGLFGAGGTGGAGGSSGGTFGGNGGSGGNAGLLALGASGGAGGSGGSALNVGGTGGVGGNGGSGGSLFGFGGAGGTGGSSGIGSSGGTGGDGGTAGVFGNGGDGGAGGFGADTGGNSSSVPNAVLIGNGGNGGNGGKAGGTPGAGGTSGLIIGENGLNGL