PE_PGRS11 Family assigned · medium auto-curated
H37Rv Rv0754 · MTBC0 - ·
584 aa · 846159–847913 (+) ·
RefSeq YP_177752.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PE-PGRS family protein PE_PGRS11 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PE-PGRS family protein PE_PGRS11. Pfam: PE (PF00934.26), PGRS (PF21526.3), His_Phos_1 (PF00300.28). |
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 |
Q79FW5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | PE-PGRS family protein PE_PGRS11 |
| EC (curated) |
EC 5.4.2.12
|
| Curated function | Induces maturation and activation of human dendritic cells (DCs), via TLR2-dependent activation of ERK1/2, p38 MAPK, and NF-kappa-B signaling pathways, and enhances the ability of DCs to stimulate CD4(+) T cells. By activating DCs, could potentially contribute to the initiation of innate immune responses during tuberculosis infection and hence regulate the clinical course of tuberculosis. Involved in resistance to oxidative stress, via TLR2-dependent activation of the PI3K-ERK1/2-NF-kappa-B signaling pathway and expression of COX-2 and Bcl2. Also abolishes H(2)O(2)-triggered activation of p38 . |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | pgmB |
| eggNOG description | Phosphoglycerate mutase family |
| Orthologous group | COG0406 |
| Gene Ontology (132) |
GO:0000287, GO:0001666, GO:0003674, GO:0003824, GO:0004619, GO:0005488, GO:0005575, GO:0005618, GO:0005623, GO:0005975, GO:0006082, GO:0006090 +120 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 | 0.516 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 7 missense, 0 nonsense, 0 frameshift |
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 | 1.4e-27 | 4–92 | PE family |
PGRS | PF21526.3 | 3.0e-08 | 154–216 | PGRS repeats |
His_Phos_1 | PF00300.28 | 5.7e-17 | 287–375 | Histidine phosphatase superfamily (branch 1) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PPE8 (PPE family protein PPE8), medium confidence from genomic context alone (score 634 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0355c PPE8 |
PPE family protein PPE8 | 634 | 634 ctx | cooccurence:634 |
Rv3347c PPE55 |
PPE family protein PPE55 | 650 | 625 ctx | cooccurence:625 |
Rv2082 hyp |
hypothetical protein | 625 | 625 ctx | cooccurence:617 |
Rv3350c PPE56 |
PPE family protein PPE56 | 620 | 620 ctx | cooccurence:620 |
Rv2819c csm5 |
CRISPR type III-associated RAMP protein Csm5 | 619 | 619 ctx | cooccurence:619 |
Rv1004c |
membrane protein | 610 | 611 ctx | cooccurence:592 |
Rv0613c hyp |
hypothetical protein | 608 | 608 ctx | cooccurence:608 |
Rv0304c PPE5 |
PPE family protein PPE5 | 696 | 594 ctx | cooccurence:594 |
Rv0341 iniB |
isoniazid inducible protein IniB | 589 | 590 ctx | cooccurence:583 |
Rv1917c PPE34 |
PPE family protein PPE34 | 589 | 589 ctx | cooccurence:589 |
Rv2209 |
integral membrane protein | 576 | 576 ctx | cooccurence:576 |
Rv0752c fadE9 |
acyl-CoA dehydrogenase FadE9 | 588 | 573 ctx | neighborhood:524 |
Rv3403c hyp |
hypothetical protein | 569 | 569 ctx | cooccurence:569 |
Rv3343c PPE54 |
PPE family protein PPE54 | 574 | 564 ctx | cooccurence:564 |
Rv1135c PPE16 |
PPE family protein PPE16 | 531 | 531 ctx | cooccurence:531 |
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_PGRS11
- Pfam (hmmscan --cut_ga): PE PF00934.26 (E=1e-27), PGRS PF21526.3 (E=3e-08), His_Phos_1 PF00300.28 (E=6e-17)
- (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_177752.1)
- Domains: Pfam-A via hmmscan --cut_ga — PE (PF00934.26), PGRS (PF21526.3), His_Phos_1 (PF00300.28)
- 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
COG0406 - Curated reference: UniProt Q79FW5 (SwissProt, reviewed; Evidence at protein 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 —
64 functional partner(s); context anchor
PPE8 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0754|PE_PGRS11 MSFVIVARDALAAAAADLAQIGSAVNAGNLAAANPTTAVAAAAADEVSAALAALFGAHAREYQAAAAQAAAYHEQFVHRLSAAATSYAVTEVTIATSLRGALGSAPASVSDGFQAFVYGPIHATGQQWINSPVGEALAPIVNAPTNVLLGRDLIGNGVTGTAAAPNGGPGGLLFGDGGAGYTGGNGGSAGLIGNGGTGGAGFAGGVGGMGGTGGWLMGNGGMGGAGGVGGNGGAGGQALLFGNGGLGGAGGAGGVDGAIGRGGWFIGTGGMATIGGGGNGQSIVIDFVRHGQTPGNAAMLIDTAVPGPGLTALGQQQAQAIANALAAKGPYAGIFDSQLIRTQQTAAPLANLLGMAPQVLPGLNEIHAGIFEDLPQISPAGLLYLVGPIAWTLGFPIVPMLAPGSTDVNGIVFNRAFTGAVQTIYDASLANPVVAADGNITSVAYSSAFTIGVGTMMNVDNPHPLLLLTHPVPNTGAVVVQGNPEGGWTLVSWDGIPVGPASLPTALFVDVRELITAPQYAAYDIWESLFTGDPAAVINAVRDGADEVGAAVVQFPHAVADDVIDATGHPYLSGLPIGLPSLIP