PE_PGRS51 Family assigned · medium auto-curated
H37Rv Rv3367 · MTBC0 - ·
588 aa · 3778568–3780334 (+) ·
RefSeq YP_177965.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PE-PGRS family protein PE_PGRS51 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PE-PGRS family protein PE_PGRS51. 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 |
L0TCB8
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | PE-PGRS family protein PE_PGRS51 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| eggNOG description | PE-PGRS family |
| Orthologous group | COG0657 |
| Gene Ontology (46) |
GO:0003674, GO:0005488, GO:0005575, GO:0005618, GO:0005623, GO:0006950, GO:0008150, GO:0009405, GO:0009605, GO:0009607, GO:0009628, GO:0009987 +34 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 | 0.675 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 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 | 9.4e-32 | 4–94 | PE family |
PGRS | PF21526.3 | 2.2e-15 | 116–186 | PGRS repeats |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: spoU (tRNA/rRNA methylase SpoU), medium confidence from genomic context alone (score 410 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3043c ctaD |
cytochrome C oxidase cytochrome 1 | 784 | 785 | experimental:783 |
Rv2200c ctaC |
cytochrome C oxidase subunit II | 784 | 784 | experimental:783 |
Rv2196 qcrB |
ubiquinol-cytochrome C reductase cytochrome subunit B | 783 | 784 | experimental:783 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 769 | 769 | experimental:747 |
Rv2193 ctaE |
cytochrome C oxidase subunit III | 747 | 748 | experimental:747 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 747 | 747 | experimental:747 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 747 | 747 | experimental:747 |
Rv2468A hyp |
hypothetical protein | 502 | 502 | experimental:484 |
Rv2876 |
transmembrane protein | 483 | 484 | experimental:484 |
Rv0432 sodC |
superoxide dismutase | 432 | 433 | experimental:431 |
Rv3584 lpqE |
lipoprotein LpqE | 431 | 431 | experimental:431 |
Rv3366 spoU |
tRNA/rRNA methylase SpoU | 410 | 410 ctx | neighborhood:410 |
Rv0538 |
membrane protein | 545 | 41 | textmining:545 |
Rv3785 hyp |
hypothetical protein | 528 | 41 | textmining:528 |
Rv3784 |
dTDP-glucose 4,6-dehydratase | 515 | 41 | textmining:515 |
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_PGRS51
- Pfam (hmmscan --cut_ga): PE PF00934.26 (E=9e-32), PGRS PF21526.3 (E=2e-15)
- (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_177965.1)
- 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
COG0657 - Curated reference: UniProt L0TCB8 (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 —
15 functional partner(s); context anchor
spoU - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3367|PE_PGRS51 MSFVVAVPEALAAAASDVANIGSALSAANAAAAAGTTGLLAAGADEVSAALASLFSGHAVSYQQVAAQATALHDQFVQALTGAGGSYALTEAANVQQNLLNAINAPTQALLGRPLIGDGAVGTASSPDGQDGGLLFGNGGAGYNSAATPGMAGGNGGNAGLIGNGGTGGSGGAGAAGGAGGSGGWLYGNGGNGGIGGNAIVAGGAGGNGGAGGAAGLWGSGGSGGQGGNGLTGNDGVNPAPVTNPALNGAAGDSNIEPQTSVLIGTQGGDGTPGGAGVNGGNGGAGGDANGNPANTSIANAGAGGNGAAGGDGGANGGAGGAGGQAASAGSSVGGDGGNGGAGGTGTNGHAGGAGGAGGAGGRGGWLVGNGGNGGNGAAGGNGAIGGTGGAGGVPANQGGNSALGTQPVGGDGGDGGNGGTGGTGGRGGDGGSGGAGGASGWLMGNGGNGGNGGTGGSGGVGGNGGIGGDGAGGGNATSTSSIPFDAHGGNGGAGGDAGHGGTGGDGGDGGHAGTGGRGGLLAGQHANSGNGGGGGTGGAGGTHGTPGSGNAGGTGTGNADSTNGGPGSDGLGGDAFNGSRGTDGNPG