PE27 Family assigned · medium auto-curated
H37Rv Rv2769c · MTBC0 - ·
275 aa · 3078158–3078985 (-) ·
RefSeq YP_177907.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PE family protein PE27 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PE family protein PE27. 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 |
Q79FA8
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | PE family protein PE27 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Polymorphic PE/PPE proteins C terminal |
| Orthologous group | 2AQVG |
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 | 2.655 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 7 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.41% of strains (597) · 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 | 1.2e-26 | 4–95 | PE family |
PPE-SVP | PF12484.14 | 1.0e-19 | 193–273 | PPE-SVP subfamily C-terminal region |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PPE43 (PPE family protein PPE43), medium confidence from genomic context alone (score 593 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2768c PPE43 |
PPE family protein PPE43 | 796 | 593 ctx | neighborhood:593 textmining:521 |
Rv2770c PPE44 |
PPE family protein PPE44 | 489 | 447 ctx | neighborhood:447 |
Rv2767c |
membrane protein | 533 | 351 | |
Rv3778c |
aminotransferase | 681 | 41 | textmining:681 |
Rv0115 hddA |
D-alpha-D-heptose-7-phosphate kinase HddA | 654 | 41 | textmining:654 |
Rv3018A PE27A |
Rv3018A, len: 28 aa. PE27A, Member of Mycobacterium tuberculosis PE family (see Brennan and Delogu, 2002), most similar to Rv0285 (102 aa), | 524 | 41 | textmining:524 |
Rv0116c ldtA |
L,D-transpeptidase LdtA | 511 | 41 | textmining:511 |
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 PE27
- Pfam (hmmscan --cut_ga): PE PF00934.26 (E=1e-26), PPE-SVP PF12484.14 (E=1e-19)
- (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_177907.1)
- 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
2AQVG - Curated reference: UniProt Q79FA8 (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 —
7 functional partner(s); context anchor
PPE43 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2769c|PE27 MSFLTTQPEELAAAAGKLETIGSAMVAQNAAAAAPTTTGVIPAAADEISVLQAPLFTAYGTLYQQVSAEAAAVYDLFVKTLGVSAGTYAATEAANSSAAASPLSGIASILGSTPGKVPSWISDIANIFNIGAGNWASAASDLLGLASGGLLPAAEEAALEEGLEGAGLSELGAAEAAVGEAPIAAGLGAAPLAAGLSRASSIGALSVPPSWAGQANLVSSTSTLQGAGWTTAAPHGAAGTVIPGMPGLASATRSSAGFGAPRYGAKPIVVPKPAV