PE_PGRS60 Family assigned · medium auto-curated
H37Rv Rv3652 · MTBC0 - ·
104 aa · 4093632–4093946 (+) ·
RefSeq YP_178001.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PE-PGRS family-related protein PE_PGRS60 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PE-PGRS family-related protein PE_PGRS60. 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 |
Q6MWV1
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | PE-PGRS family protein PE_PGRS60 |
| Curated function | Binds fibronectin. May contribute to pathogenicity. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | PE-PGRS 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) pseudogene candidate
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 10.03% of strains (14571) · 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 | 1.8e-16 | 4–60 | PE family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PE_PGRS61 (PE-PGRS family-related protein PE_PGRS61), high confidence from genomic context alone (score 781 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3653 PE_PGRS61 |
PE-PGRS family-related protein PE_PGRS61 | 781 | 781 ctx | neighborhood:781 |
Rv1089 PE10 |
PE family protein PE10; Together with PE9, induces macrophage apoptosis through human Toll-like receptor 4 (TLR4) signaling pathway. Interac | 659 | 41 | textmining:659 |
Rv2099c PE21 |
Rv2099c, (MTCY49.39c), len: 58 aa. PE21, Member of the Mycobacterium tuberculosis PE family (see Brennan and Delogu, 2002); 5'-end of Rv2098 | 652 | 41 | textmining:652 |
Rv3018A PE27A |
Rv3018A, len: 28 aa. PE27A, Member of Mycobacterium tuberculosis PE family (see Brennan and Delogu, 2002), most similar to Rv0285 (102 aa), | 651 | 41 | textmining:651 |
Rv3344c PE_PGRS49 |
PE-PGRS family protein PE_PGRS49 | 651 | 41 | textmining:651 |
Rv3512 PE_PGRS56 |
PE-PGRS family protein PE_PGRS56 | 647 | 41 | textmining:647 |
Rv0833 PE_PGRS13 |
PE-PGRS family protein PE_PGRS13 | 511 | 41 | textmining:511 |
Rv0832 PE_PGRS12 |
PE-PGRS family protein PE_PGRS12 | 510 | 41 | textmining:510 |
Rv1088 PE9 |
PE family protein PE9 | 438 | 41 | textmining:438 |
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-related protein PE_PGRS60
- Pfam (hmmscan --cut_ga): PE PF00934.26 (E=2e-16)
- (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_178001.1)
- 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 Q6MWV1 (SwissProt, reviewed; Inferred from homology)
- 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
PE_PGRS61 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3652|PE_PGRS60 MSYVIAAPEALVAAATDLATLGSTIGAANAAAAGSTTALLTAGADEVSAAIAAYSECTARPIRHSVRGRRRSMSGSCRPWPQVGAPMRPPRPPASRRCRARSIC