PE_PGRS62 Family assigned · medium auto-curated
H37Rv Rv3812 · MTBC0 - ·
504 aa · 4276571–4278085 (+) ·
RefSeq YP_178019.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PE-PGRS family protein PE_PGRS62 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PE-PGRS family protein PE_PGRS62. 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 |
L7N680
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | PE-PGRS family protein PE_PGRS62 |
| Curated function | Supports mycobacterial virulence via inhibition of phagosome maturation and host inducible nitric oxide synthase (iNOS) expression. May promote the survival within macrophages by disturbing the cytokines profiles and blocking the endoplasmic reticulum (ER) stress-mediated apoptosis. May also affect bacterial cell wall composition..; FUNCTION: Expression in Mycobacterium smegmatis, a nonpathogenic species naturally deficient in PE_PGRS genes, results in enhanced resistance to various in vitro stresses. It also leads to phagosome maturation arrest and increased survival in macrophages. |
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 | 0.979 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 10 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.23% of strains (335) · 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 | 3.9e-31 | 4–94 | PE family |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2133c hyp |
hypothetical protein | 871 | 863 | experimental:772 database:425 |
Rv2555c alaS |
alanine--tRNA ligase | 848 | 836 | experimental:570 database:622 |
Rv2101 helZ |
helicase HelZ | 779 | 766 | database:613 |
Rv1691 hyp |
hypothetical protein | 778 | 766 | experimental:454 database:583 |
Rv2267c stf3 hyp |
hypothetical protein | 778 | 766 | experimental:454 database:583 |
Rv3529c hyp |
hypothetical protein | 778 | 766 | experimental:454 database:583 |
Rv0719 rplF |
50S ribosomal protein L6 | 743 | 743 | experimental:415 database:579 |
Rv0722 rpmD |
50S ribosomal protein L30 | 740 | 740 | database:543 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 747 | 738 | database:622 |
Rv0492c |
GMC-type oxidoreductase | 739 | 729 | database:573 |
Rv3409c choD |
cholesterol oxidase | 739 | 729 | database:573 |
Rv1279 |
GMC-type oxidoreductase | 739 | 729 | database:573 |
Rv0697 mftG |
dehydrogenase | 739 | 729 | database:573 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 720 | 719 | database:624 |
Rv0703 rplW |
50S ribosomal protein L23 | 716 | 715 | database:548 |
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_PGRS62
- Pfam (hmmscan --cut_ga): PE PF00934.26 (E=4e-31)
- (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_178019.1)
- 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
COG0657 - Curated reference: UniProt L7N680 (SwissProt, reviewed; 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 — 109 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3812|PE_PGRS62 MSFVVTVPEAVAAAAGDLAAIGSTLREATAAAAGPTTGLAAAAADDVSIAVSQLFGRYGQEFQTVSNQLAAFHTEFVRTLNRGAAAYLNTESANGGQLFGQIEAGQRAVSAAAAAAPGGAYGQLVANTATNLESLYGAWSANPFPFLRQIIANQQVYWQQIAAALANAVQNFPALVANLPAAIDAAVQQFLAFNAAYYIQQIISSQIGFAQLFATTVGQGVTSVIAGWPNLAAELQLAFQQLLVGDYNAAVANLGKAMTNLLVTGFDTSDVTIGTMGTTISVTAKPKLLGPLGDLFTIMTIPAQEAQYFTNLMPPSILRDMSQNFTNVLTTLSNPNIQAVASFDIATTAGTLSTFFGVPLVLTYATLGAPFASLNAIATSAETIEQALLAGNYLGAVGALIDAPAHALDGFLNSATVLDTPILVPTGLPSPLPPTVGITLHLPFDGILVPPHPVTATISFPGAPVPIPGFPTTVTVFGTPFMGMAPLLINYIPQQLALAIKPAA