PE_PGRS28 Family assigned · medium auto-curated
H37Rv Rv1452c · MTBC0 - ·
741 aa · 1636004–1638229 (-) ·
RefSeq YP_177813.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PE-PGRS family protein PE_PGRS28 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PE-PGRS family protein PE_PGRS28. Pfam: PE (PF00934.26), PGRS (PF21526.3). |
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 |
Q79FP1
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | PE-PGRS family protein PE_PGRS28 |
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 | 0.452 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 10 synonymous, 11 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 | 9.1e-34 | 4–94 | PE family |
PGRS | PF21526.3 | 6.1e-12 | 122–191 | PGRS repeats |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2209 (integral membrane protein), high confidence from genomic context alone (score 774 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2082 hyp |
hypothetical protein | 790 | 782 ctx | cooccurence:774 |
Rv2209 |
integral membrane protein | 774 | 774 ctx | cooccurence:774 |
Rv3350c PPE56 |
PPE family protein PPE56 | 774 | 774 ctx | cooccurence:774 |
Rv0305c PPE6 |
PPE family protein PPE6 | 774 | 774 ctx | cooccurence:774 |
Rv0355c PPE8 |
PPE family protein PPE8 | 774 | 774 ctx | cooccurence:774 |
Rv0304c PPE5 |
PPE family protein PPE5 | 774 | 774 ctx | cooccurence:774 |
Rv1917c PPE34 |
PPE family protein PPE34 | 774 | 774 ctx | cooccurence:774 |
Rv3343c PPE54 |
PPE family protein PPE54 | 774 | 774 ctx | cooccurence:774 |
Rv1004c |
membrane protein | 774 | 774 ctx | cooccurence:774 |
Rv3347c PPE55 |
PPE family protein PPE55 | 774 | 774 ctx | cooccurence:774 |
Rv0341 iniB |
isoniazid inducible protein IniB | 773 | 774 ctx | cooccurence:773 |
Rv3558 PPE64 |
PPE family protein PPE64 | 773 | 773 ctx | cooccurence:773 |
Rv0755c PPE12 |
PPE family protein PPE12 | 773 | 773 ctx | cooccurence:773 |
Rv1548c PPE21 |
PPE family protein PPE21 | 773 | 773 ctx | cooccurence:773 |
Rv2356c PPE40 |
Rv2356c, (MTCY98.25), len: 615 aa. PPE40, Member of Mycobacterium tuberculosis PPE_family, highly similar to others e.g. Q10778|MTCY48.17|YF | 773 | 773 ctx | cooccurence:773 |
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_PGRS28
- Pfam (hmmscan --cut_ga): PE PF00934.26 (E=9e-34), PGRS PF21526.3 (E=6e-12)
- (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_177813.1)
- Domains: Pfam-A via hmmscan --cut_ga — PE (PF00934.26), PGRS (PF21526.3)
- 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 Q79FP1 (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 —
137 functional partner(s); context anchor
Rv2209 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1452c|PE_PGRS28 MSLVIVTPETVAAAASDVARIGSSIGVANSAAAGSTTSVLAAGADEVSAAIATLFGSHAREYQAISTQVAAFHDRFAQTLSAAVGSYVSAEATNAAPLATLEHNVLNALNAPTQALLGRPLIGDGAAGAPGTGQAGGAGGILWGNGGAGGSGAPGQVGGAGGAAGLFGTGGAGGAGGAGAAGGAGGSGGWLLGNGGVGGAGGQSLLGGATGGAGGNAGLFGVGGTGGPGGPGGPGGVGGTGGAGGLGGTLYGAGGHGGAGGPGPIGGVGGHGGVGGAAGLLGVGGHGGAGGHGAEGVAGAAGEDLSPHGTSGGVGGDAGDGGTGGRGGWLAGAGGAGGAGGVGGTGGAGGAGFSRALIVAGDNGGDGGNGGMGGAGGAGGPGGAGGLISLLGGQGAGGAGGTGGAGGVGGDRGAGGPGNQAFNAGAGGAGGHGGDPGAGGAGGTGGAGSITGAQGAIGATPTSGGNGGAGGNGANATTAGTNGANGGPGGHGGLVGNGGAGGNGANGAAGTNASDSGAVGGKGNSGGNGGQGGAGGDGGTLAGNGGAGGTGGRGADGGLGGSGAEGANATTAGERGQDGGKGGNGGVGGTGGNAVAPGANGGHGGNGGNPGFSGAGGLGGLSGDGVTRAAQGATPDFADTGGKGGNGGNGANAVAPGGTGASGGAGGNAGAGGKGGENIIGDGGGGNGGAGGKGGAGTLLGLTVFGDNGGAGVLGDSTDPDGSGGAGGAGGAGGAGGDPTI