PE_PGRS40 Family assigned · medium auto-curated
H37Rv Rv2371 · MTBC0 - ·
61 aa · 2651753–2651938 (+) ·
RefSeq YP_177875.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PE-PGRS family protein PE_PGRS40 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PE-PGRS family protein PE_PGRS40. Pfam: PE (PF00934.26). |
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 |
Q79FE9
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | PE-PGRS family protein PE_PGRS40 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | PE family |
| Orthologous group | COG3391 |
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 | 3.2e-14 | 4–60 | PE family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ybeY (endoribonuclease), medium confidence from genomic context alone (score 497 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2370c hyp |
hypothetical protein | 533 | 532 ctx | neighborhood:532 |
Rv2367c ybeY |
endoribonuclease | 497 | 497 ctx | neighborhood:497 |
Rv2368c phoH1 |
phosphate starvation-inducible protein PhoH | 497 | 497 ctx | neighborhood:497 |
Rv2365c hyp |
hypothetical protein | 497 | 497 ctx | neighborhood:497 |
Rv2369c hyp |
hypothetical protein | 497 | 497 ctx | neighborhood:497 |
Rv2366c |
transmembrane protein | 497 | 497 ctx | neighborhood:497 |
Rv0878c PPE13 |
PPE family protein PPE13 | 656 | 41 | textmining:656 |
Rv2408 PE24 |
PE family protein PE24 | 625 | 41 | textmining:625 |
Rv0388c PPE9 |
Rv0388c, (MTV036.23c), len: 180 aa. PPE9, Member of the Mycobacterium tuberculosis PPE family, highly similar to others e.g. MTCY10G2_10|Z92 | 579 | 41 | textmining:579 |
Rv0354c PPE7 |
PPE family protein PPE7 | 546 | 41 | textmining:546 |
Rv1146 mmpL13b |
transmembrane transport protein | 544 | 41 | textmining:544 |
Rv0304c PPE5 |
PPE family protein PPE5 | 510 | 41 | textmining:510 |
Rv1807 PPE31 |
Rv1807, (MTV049.29), len: 399 aa. PPE31, Member of the Mycobacterium tuberculosis PPE family of glycine-rich proteins, most similar to Rv178 | 410 | 41 | textmining:411 |
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-PGRS family protein PE_PGRS40
- Pfam (hmmscan --cut_ga): PE PF00934.26 (E=3e-14)
- (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_177875.1)
- Domains: Pfam-A via hmmscan --cut_ga — PE (PF00934.26)
- 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
COG3391 - Curated reference: UniProt Q79FE9 (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 —
13 functional partner(s); context anchor
ybeY - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2371|PE_PGRS40 MSLVSVAPELVVTAVPDVARIGSSIGAPDTAAAARPTTSVLAAGADEVSADVVALFGWVAR