PE9 Family assigned · medium auto-curated
H37Rv Rv1088 · MTBC0 - ·
144 aa · 1214513–1214947 (+) ·
RefSeq YP_177784.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PE family protein PE9 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PE family protein PE9. 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 |
Q79FS8
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | PE family protein PE9 |
| Curated function | Together with PE10, induces macrophage apoptosis through human Toll-like receptor 4 (TLR4) signaling pathway. Interaction with TLR4 leads to increased levels of phospho-IRF-3, increase in the transcript levels of IFN-beta and pro-apoptotic genes, up-regulation of IL-10, down-regulation of IL-1b and enhanced levels of macrophage apoptosis. |
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 (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.719 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 1.15% of strains (1675) · 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 | 7.2e-28 | 4–88 | PE family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PE10 (PE family protein PE10; Together with PE9, induces macrophage apoptosis through human Toll-like receptor 4 (TLR4) signaling pathway. Interac), high confidence from genomic context alone (score 773 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1089 PE10 |
PE family protein PE10; Together with PE9, induces macrophage apoptosis through human Toll-like receptor 4 (TLR4) signaling pathway. Interac | 988 | 773 ctx | neighborhood:773 textmining:953 |
Rv1087A |
Rv1087A, len: 106 aa (fragment). Conserved hypothetical protein, highly similar to C-terminus of near ORF O53434|YA86_MYCTU|Rv1086|MT1118|MT | 473 | 473 ctx | neighborhood:473 |
Rv3602c panC |
pantothenate synthetase | 437 | 437 | experimental:423 |
Rv0992c |
5-formyltetrahydrofolate cyclo-ligase | 422 | 422 | coexpression:422 |
Rv2205c hyp |
hypothetical protein | 414 | 415 | coexpression:415 |
Rv2190c ripC |
endopeptidase | 414 | 70 | |
Rv0833 PE_PGRS13 |
PE-PGRS family protein PE_PGRS13 | 543 | 58 | textmining:536 |
Rv2126c PE_PGRS37 |
PE-PGRS family protein PE_PGRS37 | 463 | 58 | textmining:454 |
Rv0754 PE_PGRS11 |
PE-PGRS family protein PE_PGRS11 | 412 | 43 | textmining:411 |
Rv1115 hyp |
hypothetical protein | 651 | 41 | textmining:651 |
Rv3746c PE34 |
PE family protein PE34 | 630 | 41 | textmining:630 |
Rv3652 PE_PGRS60 |
PE-PGRS family-related protein PE_PGRS60 | 438 | 41 | textmining:438 |
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 family protein PE9
- Pfam (hmmscan --cut_ga): PE PF00934.26 (E=7e-28)
- (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_177784.1)
- 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 Q79FS8 (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 —
12 functional partner(s); context anchor
PE10 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1088|PE9 MSYMIATPAALTAAATDIDGIGSAVSVANAAAVAATTGVLAAGGDEVLAAIARLFNANAEEYHALSAQVAAFQTLFVRTLTGGCGVFRRRRGRQCVTAAEHRAAGAGRRQRRRRSGDGQWRLRQQRHFGCGGQPEFRQHSEHRR