PPE11 Family assigned · medium auto-curated
H37Rv Rv0453 · MTBC0 - ·
518 aa · 543174–544730 (+) ·
RefSeq YP_177727.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PPE family protein PPE11 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PPE family protein PPE11. Pfam: PPE (PF00823.26), PPE-PPW (PF18878.6). |
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 |
P9WI39
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | PPE family protein PPE11 |
| Curated function | May play an important role in the persistence of mycobacteria in host cells. May regulate the innate immune response of macrophages by promoting the production of pro-inflammatory cytokines and inhibiting the production of anti-inflammatory cytokines. Promotes the death of macrophages during infection. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
N Cell motility
|
|---|---|
| eggNOG description | PPE family |
| Orthologous group | COG5651 |
| Gene Ontology (9) |
GO:0005575, GO:0005576, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0044424, GO:0044444, GO:0044464
|
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 | 0.717 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
PPE | PF00823.26 | 1.0e-60 | 7–169 | PPE family |
PPE-PPW | PF18878.6 | 3.8e-17 | 463–509 | PPE-PPW subfamily C-terminal region |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0454 (Conserved hypothetical protein; Rv0454, (MTV037.18), len: 116 aa (start uncertain). Conserved hypothetical protein, showing similarity with ), medium confidence from genomic context alone (score 523 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0454 |
Conserved hypothetical protein; Rv0454, (MTV037.18), len: 116 aa (start uncertain). Conserved hypothetical protein, showing similarity with | 523 | 523 ctx | neighborhood:519 |
Rv0452 |
transcriptional regulator | 402 | 402 ctx | neighborhood:400 |
Rv0265c |
iron ABC transporter substrate-binding lipoprotein | 805 | 51 | textmining:803 |
Rv2120c |
integral membrane protein | 548 | 45 | textmining:547 |
Rv3746c PE34 |
PE family protein PE34 | 655 | 41 | textmining:655 |
Rv2396 PE_PGRS41 |
acid and phagosome regulated protein AprC | 439 | 41 | textmining:439 |
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 PPE11
- Pfam (hmmscan --cut_ga): PPE PF00823.26 (E=1e-60), PPE-PPW PF18878.6 (E=4e-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_177727.1)
- Domains: Pfam-A via hmmscan --cut_ga — PPE (PF00823.26), PPE-PPW (PF18878.6)
- 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 P9WI39 (SwissProt, reviewed; Inferred from homology)
- 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 —
6 functional partner(s); context anchor
Rv0454 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0453|PPE11 MTSALIWMASPPEVHSALLSSGPGPGPVLAAATGWSSLGREYAAVAEELGALLAAVQAGVWQGPSAESFAAACLPYLSWLTQASADCAAAAARLEAVTAAYAAALVAMPTLAELAANHATHGAMVATNFFGINTIPIAVNEADYVRMWLQAATTMATYQAVADSAVRSIPDSVPPPRILKSNAQSQHSSSNNSGGADPVDDFIAEILKIITGGRVIWDPEAGTVNGLPYDAYTNPGTLMWWIARSLELLQDFQEFAKLLFTNPVKAFQFLVDLILFDWPTHMLQLATWLAENPQLLVAALTPAISGLGAVSGLAGLTGLVPQPPVVPAPAPDAVVPTVLPLAGTATPTTAPASAPAAGAAPGPPAGTATATSASVPTSAGGFPPYLVGSGPGIDFDAGTPAGSRRAQPAADNVTAVAAAQVSARHQARRRRRAAAKERGNADEFVDMDSGPAIPPSGERDAWASNSGVGGLGFAGTASNETVAAPAGLTTLADDEFQCGPRMPMLPGAWDLGTWDRGD