PE8 Family assigned · medium auto-curated
H37Rv Rv1040c · MTBC0 - ·
275 aa · 1162549–1163376 (-) ·
RefSeq YP_177779.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PE family protein PE8 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PE family protein PE8. Pfam: PE (PF00934.26), PPE-SVP (PF12484.14). |
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 |
L7N667
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | PE family protein PE8 |
| Curated function | Promotes the intracellular survival of recombinant Mycobacterium within macrophages by regulating host inflammatory cytokines production and inhibiting cell late apoptosis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Polymorphic PE/PPE proteins C terminal |
| Orthologous group | 29WFN |
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 | 0.502 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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 | 1.0e-26 | 5–93 | PE family |
PPE-SVP | PF12484.14 | 6.0e-20 | 192–272 | PPE-SVP subfamily C-terminal region |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PPE15 (PPE family protein PPE15), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1039c PPE15 |
PPE family protein PPE15 | 999 | 1000 ctx | neighborhood:594 experimental:999 textmining:437 |
Rv2768c PPE43 |
PPE family protein PPE43 | 907 | 899 | experimental:891 |
Rv2770c PPE44 |
PPE family protein PPE44 | 904 | 899 | experimental:891 |
Rv1794 espG5 hyp |
hypothetical protein | 898 | 898 | experimental:898 |
Rv1038c esxJ |
ESAT-6 like protein EsxJ | 477 | 366 | |
Rv1037c esxI |
ESAT-6 like protein EsxI | 484 | 340 | |
Rv3621c PPE65 |
PPE family protein PPE65 | 559 | 291 | textmining:404 |
Rv0355c PPE8 |
PPE family protein PPE8 | 475 | 291 | |
Rv3478 PPE60 |
PE family protein PPE60 | 414 | 291 | |
Rv2352c PPE38 |
PPE family protein PPE38 | 409 | 291 | |
Rv2633c hyp |
hypothetical protein | 519 | 41 | textmining:519 |
Rv1004c |
membrane protein | 515 | 41 | textmining:515 |
Rv3289c |
transmembrane protein | 515 | 41 | textmining:515 |
Rv2632c hyp |
hypothetical protein | 511 | 41 | textmining:511 |
Rv2442c rplU |
50S ribosomal protein L21 | 510 | 41 | textmining:510 |
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 PE8
- Pfam (hmmscan --cut_ga): PE PF00934.26 (E=1e-26), PPE-SVP PF12484.14 (E=6e-20)
- (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_177779.1)
- Domains: Pfam-A via hmmscan --cut_ga — PE (PF00934.26), PPE-SVP (PF12484.14)
- 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
29WFN - Curated reference: UniProt L7N667 (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 —
20 functional partner(s); context anchor
PPE15 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1040c|PE8 MSFLKTVPEELTAAAAQLGTIGAAMAAQNAAAAAPTTAIAPAALDEVSALQAALFTAYGTFYQQVSAEAQAMHDMFVNTLGISAGTYGVTESLNSSAAASPLSGITGEASAIIQATTGLFPPELSGGIGNILNIGAGNWASATSTLIGLAGGGLLPAEEAAEAASALGGEAALGELGALGAAEAALGEAGIAAGLGSASAIGMLSVPPAWAGQATLVSTTSTLPGAGWTAAAPQAAAGTFIPGMPGVASAARNSAGFGAPRYGVKPIVMPKPATV