PE_PGRS38 Family assigned · medium auto-curated
H37Rv Rv2162c · MTBC0 - ·
532 aa · 2423240–2424838 (-) ·
RefSeq YP_177865.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PE-PGRS family protein PE_PGRS38 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PE-PGRS family protein PE_PGRS38. 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 |
L7N6A1
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | PE-PGRS family protein PE_PGRS38 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| eggNOG description | PE family |
| Orthologous group | COG0657 |
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 | 1.443 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 | 8.9e-35 | 4–94 | PE family |
PGRS | PF21526.3 | 4.8e-12 | 116–184 | PGRS repeats |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rsmH (rRNA small subunit methyltransferase H), medium confidence from genomic context alone (score 443 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2161c hyp |
hypothetical protein | 905 | 540 ctx | neighborhood:540 textmining:803 |
Rv2165c rsmH |
rRNA small subunit methyltransferase H | 443 | 443 ctx | neighborhood:443 |
Rv2164c hyp |
hypothetical protein | 443 | 443 ctx | neighborhood:443 |
Rv2163c pbpB |
penicillin-binding membrane protein PbpB | 443 | 443 ctx | neighborhood:443 |
Rv2166c mraZ |
transcriptional regulator MraZ | 440 | 440 ctx | neighborhood:440 |
Rv2160c |
Rv2160c, (MTCY270.08), len: 113 aa. Conserved hypothetical protein, possibly a TetR-family transcriptional regulator, similar to C-terminal | 863 | 336 | textmining:803 |
Rv2159c hyp |
hypothetical protein | 805 | 57 | textmining:802 |
Rv2158c murE |
UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase | 436 | 50 | textmining:431 |
Rv2151c ftsQ |
cell division protein FtsQ | 435 | 49 | textmining:431 |
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_PGRS38
- Pfam (hmmscan --cut_ga): PE PF00934.26 (E=9e-35), PGRS PF21526.3 (E=5e-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_177865.1)
- 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
COG0657 - Curated reference: UniProt L7N6A1 (TrEMBL, unreviewed; Evidence at protein level)
- 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 —
9 functional partner(s); context anchor
rsmH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2162c|PE_PGRS38 MSFVIAAPEVMAAAATDLANIGSSISAASAAAAGPTMGILAAGADEVSVAISALFGSHAQGYQTLSAQLAAYHNQFVRALNAGAGSYASAEAANVQQTLLNAINAPTQTLLGRPLIGNGADGGPGQNGGPGGLLYGNGGNGGAGDTANPNGGNGGSAGLIGNGGAGGAGAATGAGGAGGNGGWLYGNGGPGGAAGLGTAGGVSPAGGAGGAAGLWGHGGAGGAGGSASGAPGAGGAGGDGGRGGLLYGDGGAGGAGGNGSNGVTGVHGGNGGAGGAAGLIGNGGAGGDGGNGGLSNTGASGGAGGAGGAALIGNGGDGGHGGNGGHGNSGGAGGAGGAGGAGGAGGHVGLIGNGGNGGAGGNGGNDNSSTLADAGSGGAGAAGGNGGLFYGNGGVGGRGGNGGFSSAGTSGGDGGIGGAGGIGGLIGSGGGGGDGGNGGQAPTPGNAGDGGAGGNARLIGDGGRGGNGGEGGDGPPGVKGDGGNGGNGGNAVVIGNGGNGGAGGFGIPVGSGGAGGSRGVLFGTPGANGADG