PE_PGRS6 Family assigned · medium auto-curated
H37Rv Rv0532 · MTBC0 - ·
594 aa · 622793–624577 (+) ·
RefSeq YP_177736.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PE-PGRS family protein PE_PGRS6 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PE-PGRS family protein PE_PGRS6. 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 |
L0T3X8
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | PE_PGRS6 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| eggNOG description | PE family |
| Orthologous group | COG0657 |
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 | 0.278 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 13 synonymous, 9 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 13.09% of strains (19010) · 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 | 5.0e-33 | 4–94 | PE family |
PGRS | PF21526.3 | 4.7e-10 | 116–184 | PGRS repeats |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0531 (membrane protein), medium confidence from genomic context alone (score 478 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0531 |
membrane protein | 478 | 478 ctx | neighborhood:478 |
Rv0198c zmp1 |
zinc metalloprotease | 407 | 407 | |
Rv2089c pepE |
dipeptidase PepE | 545 | 45 | textmining:543 |
Rv1937 |
oxygenase | 801 | 43 | textmining:801 |
Rv1875 hyp |
hypothetical protein | 656 | 43 | textmining:656 |
Rv1526c |
glycosyltransferase | 801 | 41 | textmining:801 |
Rv1924c hyp |
hypothetical protein | 801 | 41 | textmining:801 |
Rv1728c hyp |
hypothetical protein | 654 | 41 | textmining:654 |
Rv2971 |
oxidoreductase | 528 | 41 | textmining:528 |
Rv1626 pdtaR |
two-component system transcriptional regulator | 519 | 41 | textmining:519 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 517 | 41 | textmining:517 |
Rv3150 nuoF |
NADH-quinone oxidoreductase subunit F | 513 | 41 | textmining:513 |
Rv1265 hyp |
hypothetical protein | 511 | 41 | textmining:511 |
Rv3003c ilvB1 |
acetolactate synthase large subunit IlvB | 510 | 41 | textmining:510 |
Rv0544c |
transmembrane protein | 440 | 41 | textmining:440 |
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_PGRS6
- Pfam (hmmscan --cut_ga): PE PF00934.26 (E=5e-33), PGRS PF21526.3 (E=5e-10)
- (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_177736.1)
- 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 L0T3X8 (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
Rv0531 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0532|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