PE_PGRS16 Family assigned · medium auto-curated
H37Rv Rv0977 · MTBC0 - ·
923 aa · 1090373–1093144 (+) ·
RefSeq YP_177773.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PE-PGRS family protein PE_PGRS16 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PE-PGRS family protein PE_PGRS16. Pfam: PE (PF00934.26), PGRS (PF21526.3), PE-PGRS_C (PF20729.3). |
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 |
Q79FU3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | PE-PGRS family protein PE_PGRS16 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| eggNOG description | acetylesterase activity |
| 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) pseudogene candidate
| pN/pS | 0.291 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 6 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 9.45% of strains (13721) · 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 | 8.0e-28 | 4–92 | PE family |
PGRS | PF21526.3 | 2.6e-10 | 121–187 | PGRS repeats |
PE-PGRS_C | PF20729.3 | 3.6e-91 | 657–920 | PE-PGRS C-terminal aspartyl peptidase-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PPE34 (PPE family protein PPE34), high confidence from genomic context alone (score 771 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2082 hyp |
hypothetical protein | 838 | 833 ctx | cooccurence:773 |
Rv1917c PPE34 |
PPE family protein PPE34 | 771 | 771 ctx | cooccurence:771 |
Rv3343c PPE54 |
PPE family protein PPE54 | 810 | 770 ctx | cooccurence:770 |
Rv3899c hyp |
hypothetical protein | 778 | 770 ctx | cooccurence:688 |
Rv0355c PPE8 |
PPE family protein PPE8 | 775 | 770 ctx | cooccurence:770 |
Rv3350c PPE56 |
PPE family protein PPE56 | 770 | 770 ctx | cooccurence:770 |
Rv3347c PPE55 |
PPE family protein PPE55 | 770 | 770 ctx | cooccurence:770 |
Rv1004c |
membrane protein | 772 | 769 ctx | cooccurence:767 |
Rv0305c PPE6 |
PPE family protein PPE6 | 781 | 767 ctx | cooccurence:767 |
Rv1753c PPE24 |
PPE family protein PPE24 | 828 | 766 ctx | cooccurence:766 |
Rv0304c PPE5 |
PPE family protein PPE5 | 765 | 765 ctx | cooccurence:765 |
Rv3879c espK |
ESX-1 secretion-associated protein EspK | 763 | 764 ctx | cooccurence:723 |
Rv2209 |
integral membrane protein | 763 | 763 ctx | cooccurence:763 |
Rv0755c PPE12 |
PPE family protein PPE12 | 858 | 762 ctx | cooccurence:762 textmining:431 |
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 | 760 | 760 ctx | cooccurence:760 |
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_PGRS16
- Pfam (hmmscan --cut_ga): PE PF00934.26 (E=8e-28), PGRS PF21526.3 (E=3e-10), PE-PGRS_C PF20729.3 (E=4e-91)
- (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_177773.1)
- Domains: Pfam-A via hmmscan --cut_ga — PE (PF00934.26), PGRS (PF21526.3), PE-PGRS_C (PF20729.3)
- 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 Q79FU3 (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 —
131 functional partner(s); context anchor
PPE34 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0977|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