PPE39 Family assigned · medium auto-curated
H37Rv Rv2353c · MTBC0 - ·
354 aa · 2634528–2635592 (-) ·
RefSeq YP_177871.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PPE family protein PPE39 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PPE family protein PPE39. Pfam: Pentapeptide_2 (PF01469.25). |
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 |
Q79FF3
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | PPE family protein PPE39 |
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.132 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 3 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 |
|---|---|---|---|---|
Pentapeptide_2 | PF01469.25 | 5.2e-10 | 7–45 | Pentapeptide repeats (8 copies) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PE_PGRS23 (PE-PGRS family protein PE_PGRS23), high confidence from genomic context alone (score 763 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1243c PE_PGRS23 |
PE-PGRS family protein PE_PGRS23 | 763 | 763 ctx | cooccurence:763 |
Rv0124 PE_PGRS2 |
PE-PGRS family protein PE_PGRS2 | 743 | 743 ctx | cooccurence:743 |
Rv1004c |
membrane protein | 732 | 732 ctx | cooccurence:732 |
Rv2126c PE_PGRS37 |
PE-PGRS family protein PE_PGRS37 | 737 | 730 ctx | cooccurence:730 |
Rv2853 PE_PGRS48 |
PE-PGRS family protein PE_PGRS48 | 729 | 729 ctx | cooccurence:729 |
Rv3864 espE |
ESX-1 secretion-associated protein EspE | 724 | 725 ctx | cooccurence:722 |
Rv0341 iniB |
isoniazid inducible protein IniB | 695 | 696 ctx | cooccurence:695 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 676 | 676 ctx | cooccurence:676 |
Rv2082 hyp |
hypothetical protein | 671 | 672 ctx | cooccurence:669 |
Rv0613c hyp |
hypothetical protein | 669 | 669 ctx | cooccurence:668 |
Rv3879c espK |
ESX-1 secretion-associated protein EspK | 650 | 650 ctx | cooccurence:650 |
Rv2209 |
integral membrane protein | 647 | 647 ctx | cooccurence:645 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 634 | 634 ctx | cooccurence:634 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 619 | 619 ctx | cooccurence:619 |
Rv0872c PE_PGRS15 |
PE-PGRS family protein PE_PGRS15 | 612 | 612 ctx | cooccurence:612 |
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 PPE39
- Pfam (hmmscan --cut_ga): Pentapeptide_2 PF01469.25 (E=5e-10)
- (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_177871.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pentapeptide_2 (PF01469.25)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt Q79FF3 (TrEMBL, unreviewed; Predicted)
- 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 —
52 functional partner(s); context anchor
PE_PGRS23 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2353c|PPE39 MPGRFRNFGSQNLGSGNIGSTNVGSGNIGSTNVGSGNIGDTNFGNGNNGNFNFGSGNTGSNNIGFGNTGSGNFGFGNTGNNNIGIGLTGDGQIGIGGLNSGSGNIGFGNSGTGNVGLFNSGTGNVGFGNSGTANTGFGNAGNVNTGFWNGGSTNTGLANAGAGNTGFFDAGNYNFGSLNAGNINSSFGNSGDGNSGFLNAGDVNSGVGNAGDVNTGLGNSGNINTGGFNPGTLNTGFFSAMTQAGPNSGFFNAGTGNSGFGHNDPAGSGNSGIQNSGFGNSGYVNTSTTSMFGGNSGVLNTGYGNSGFYNAAVNNTGIFVTGVMSSGFFNFGTGNSGLLVSGNGLSGFFKNLFG