PE_PGRS42 Family assigned · medium auto-curated
H37Rv Rv2487c · MTBC0 - ·
694 aa · 2795301–2797385 (-) ·
RefSeq YP_177886.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PE-PGRS family protein PE_PGRS42 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PE-PGRS family protein PE_PGRS42. 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 |
I6XEF1
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | PE-PGRS family protein PE_PGRS42 |
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 | 0.515 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 10 synonymous, 13 missense, 0 nonsense, 4 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 10.36% of strains (15037) · convergent |
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 | 3.7e-33 | 4–93 | PE family |
PGRS | PF21526.3 | 5.2e-12 | 115–183 | PGRS repeats |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3435c (transmembrane protein), high confidence from genomic context alone (score 715 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2305 hyp |
hypothetical protein | 765 | 765 ctx | cooccurence:765 |
Rv3091 hyp |
hypothetical protein | 749 | 749 ctx | cooccurence:749 |
Rv2082 hyp |
hypothetical protein | 756 | 748 ctx | cooccurence:738 |
Rv1060 hyp |
hypothetical protein | 718 | 718 ctx | cooccurence:718 |
Rv3435c |
transmembrane protein | 715 | 715 ctx | cooccurence:715 |
Rv2488c |
LuxR family transcriptional regulator | 713 | 712 ctx | neighborhood:556 |
Rv0341 iniB |
isoniazid inducible protein IniB | 697 | 698 ctx | cooccurence:697 |
Rv3347c PPE55 |
PPE family protein PPE55 | 685 | 685 ctx | cooccurence:685 |
Rv3350c PPE56 |
PPE family protein PPE56 | 681 | 681 ctx | cooccurence:681 |
Rv1917c PPE34 |
PPE family protein PPE34 | 680 | 680 ctx | cooccurence:680 |
Rv0355c PPE8 |
PPE family protein PPE8 | 680 | 680 ctx | cooccurence:680 |
Rv3343c PPE54 |
PPE family protein PPE54 | 674 | 674 ctx | cooccurence:674 |
Rv1753c PPE24 |
PPE family protein PPE24 | 650 | 650 ctx | cooccurence:650 |
Rv3843c |
transmembrane protein | 650 | 650 ctx | cooccurence:650 |
Rv2209 |
integral membrane protein | 648 | 648 ctx | cooccurence:648 |
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_PGRS42
- Pfam (hmmscan --cut_ga): PE PF00934.26 (E=4e-33), 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_177886.1)
- 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 I6XEF1 (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 —
81 functional partner(s); context anchor
Rv3435c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2487c|PE_PGRS42 MSLVIATPQLLATAALDLASIGSQVSAANAAAAMPTTEVVAAAADEVSAAIAGLFGAHARQYQALSVQVAAFHEQFVQALTAAAGRYASTEAAVERSLLGAVNAPTEALLGRPLIGNGADGTAPGQPGAAGGLLFGNGGNGAAGGFGQTGGSGGAAGLIGNGGNGGAGGTGAAGGAGGNGGWLWGNGGNGGVGGTSVAAGIGGAGGNGGNAGLFGHGGAGGTGGAGLAGANGVNPTPGPAASTGDSPADVSGIGDQTGGDGGTGGHGTAGTPTGGTGGDGATATAGSGKATGGAGGDGGTAAAGGGGGNGGDGGVAQGDIASAFGGDGGNGSDGVAAGSGGGSGGAGGGAFVHIATATSTGGSGGFGGNGAASAASGADGGAGGAGGNGGAGGLLFGDGGNGGAGGAGGIGGDGATGGPGGSGGNAGIARFDSPDPEAEPDVVGGKGGDGGKGGSGLGVGGAGGTGGAGGNGGAGGLLFGNGGNGGNAGAGGDGGAGVAGGVGGNGGGGGTATFHEDPVAGVWAVGGVGGDGGSGGSSLGVGGVGGAGGVGGKGGASGMLIGNGGNGGSGGVGGAGGVGGAGGDGGNGGSGGNASTFGDENSIGGAGGTGGNGGNGANGGNGGAGGIAGGAGGSGGFLSGAAGVSGADGIGGAGGAGGAGGAGGSGGEAGAGGLTNGPGSPGVSGTEGMAGAPG