PPE41 Family assigned · medium auto-curated
H37Rv Rv2430c · MTBC0 - ·
194 aa · 2727336–2727920 (-) ·
RefSeq YP_177881.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PPE family protein PPE41 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PPE family protein PPE41. Pfam: PPE (PF00823.26). |
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 |
Q79FE1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | PPE family protein PPE41 |
| Curated function | The PE25/PPE41 dimer induces both a strong humoral and cellular immune response. The dimer induces necrosis, but not apoptosis, in mouse macrophage cells. It also induces activation and maturation of mouse dendritic cells and drives Th2-biased immune responses. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
N Cell motility
|
|---|---|
| eggNOG description | PPE family |
| Orthologous group | COG5651 |
| Gene Ontology (2) |
GO:0005575, GO:0005576
|
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 | 0.588 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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 |
|---|---|---|---|---|
PPE | PF00823.26 | 2.0e-52 | 2–165 | PPE family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PE25 (PE family protein PE25), high confidence from genomic context alone (score 964 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1794 espG5 hyp |
hypothetical protein | 999 | 999 | experimental:999 textmining:880 |
Rv2431c PE25 |
PE family protein PE25 | 999 | 964 ctx | neighborhood:675 experimental:893 textmining:996 |
Rv2432c hyp |
hypothetical protein | 417 | 417 ctx | neighborhood:408 |
Rv2434c |
transmembrane protein | 415 | 415 ctx | neighborhood:408 |
Rv2433c nrtS hyp |
hypothetical protein | 412 | 412 ctx | neighborhood:408 |
Rv2435c |
cyclase | 409 | 410 ctx | neighborhood:406 |
Rv0288 esxH |
ESAT-6-like protein EsxH | 411 | 61 | |
Rv1793 esxN |
ESAT-6 like protein EsxN | 678 | 55 | textmining:674 |
Rv3874 esxB |
ESAT-6-like protein EsxB | 537 | 55 | textmining:531 |
Rv3875 esxA |
ESAT-6 protein EsxA | 517 | 55 | textmining:510 |
Rv2347c esxP |
ESAT-6 like protein EsxP | 407 | 55 | |
Rv1783 eccC5 |
ESX-5 type VII secretion system protein EccC5 | 435 | 47 | textmining:432 |
Rv1818c PE_PGRS33 |
PE-PGRS family protein PE_PGRS33 | 668 | 41 | textmining:668 |
Rv1791 PE19 |
PE family protein PE19 | 658 | 41 | textmining:659 |
Rv1169c lipX |
lipase LipX | 567 | 41 | textmining:568 |
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): PPE family protein PPE41
- Pfam (hmmscan --cut_ga): PPE PF00823.26 (E=2e-52)
- (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_177881.1)
- Domains: Pfam-A via hmmscan --cut_ga — PPE (PF00823.26)
- 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
COG5651 - Curated reference: UniProt Q79FE1 (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 —
23 functional partner(s); context anchor
PE25 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2430c|PPE41 MHFEAYPPEVNSANIYAGPGPDSMLAAARAWRSLDVEMTAVQRSFNRTLLSLMDAWAGPVVMQLMEAAKPFVRWLTDLCVQLSEVERQIHEIVRAYEWAHHDMVPLAQIYNNRAERQILIDNNALGQFTAQIADLDQEYDDFWDEDGEVMRDYRLRVSDALSKLTPWKAPPPIAHSTVLVAPVSPSTASSRTDT