PPE13 Family assigned · medium auto-curated
H37Rv Rv0878c · MTBC0 - ·
443 aa · 976872–978203 (-) ·
RefSeq YP_177764.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PPE family protein PPE13 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PPE family protein PPE13. Pfam: PPE (PF00823.26), Pentapeptide_2 (PF01469.25). |
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 |
P9WI35
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Uncharacterized PPE family protein PPE13 |
UniProt still lists this protein as Uncharacterized PPE family protein PPE13; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
N Cell motility
|
|---|---|
| eggNOG description | PPE family |
| Orthologous group | COG5651 |
| Gene Ontology (9) |
GO:0008150, GO:0040007, GO:0044110, GO:0044116, GO:0044117, GO:0044119, GO:0044403, GO:0044419, GO:0051704
|
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 | 0.56 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 8 missense, 0 nonsense, 13 frameshift |
| Disruption | 13 distinct premature-stop/frameshift site(s); most common in 14.59% of strains (21192) · 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 |
|---|---|---|---|---|
PPE | PF00823.26 | 8.8e-60 | 2–169 | PPE family |
Pentapeptide_2 | PF01469.25 | 3.2e-08 | 290–326 | Pentapeptide repeats (8 copies) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PE_PGRS28 (PE-PGRS family protein PE_PGRS28), high confidence from genomic context alone (score 770 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2082 hyp |
hypothetical protein | 773 | 774 ctx | cooccurence:769 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 770 | 770 ctx | cooccurence:770 |
Rv0124 PE_PGRS2 |
PE-PGRS family protein PE_PGRS2 | 769 | 769 ctx | cooccurence:769 |
Rv1004c |
membrane protein | 768 | 768 ctx | cooccurence:768 |
Rv0872c PE_PGRS15 |
PE-PGRS family protein PE_PGRS15 | 767 | 767 ctx | cooccurence:767 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 767 | 767 ctx | cooccurence:767 |
Rv2853 PE_PGRS48 |
PE-PGRS family protein PE_PGRS48 | 765 | 765 ctx | cooccurence:765 |
Rv2209 |
integral membrane protein | 764 | 764 ctx | cooccurence:762 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 762 | 762 ctx | cooccurence:762 |
Rv1243c PE_PGRS23 |
PE-PGRS family protein PE_PGRS23 | 758 | 758 ctx | cooccurence:758 |
Rv2942 mmpL7 |
transmembrane transport protein MmpL7 | 753 | 754 ctx | cooccurence:749 |
Rv3864 espE |
ESX-1 secretion-associated protein EspE | 751 | 752 ctx | cooccurence:750 |
Rv0977 PE_PGRS16 |
PE-PGRS family protein PE_PGRS16 | 750 | 750 ctx | cooccurence:750 |
Rv3903c cpnT hyp |
hypothetical protein | 748 | 749 ctx | cooccurence:717 |
Rv2945c lppX |
lipoprotein LppX | 737 | 738 ctx | cooccurence:734 |
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): PPE family protein PPE13
- Pfam (hmmscan --cut_ga): PPE PF00823.26 (E=9e-60), Pentapeptide_2 PF01469.25 (E=3e-08)
- (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_177764.1)
- Domains: Pfam-A via hmmscan --cut_ga — PPE (PF00823.26), Pentapeptide_2 (PF01469.25)
- 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
COG5651 - Curated reference: UniProt P9WI35 (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 —
98 functional partner(s); context anchor
PE_PGRS28 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0878c|PPE13 MNFMVLPPEVNSARIYAGAGPAPMLAAAVAWDGLAAELGMAAASFSLLISGLTAGPGSAWQGPAAAAMAAAAAPYLSWLNAATARAEGAAAGAKAAAAVYEAARAATAHPALVAANRNQLLSLVLSNLFGQNLPAIAATEASYEQLWAQDVAAMVGYHGGASTVASQLTPWQQLLSVLPPVVTAAPAGAVGVPAALAIPALGVENIGVGNFLGIGNIGNNNVGSGNTGDYNFGIGNIGNANLGNGNIGNANLGSGNAGFFNFGNGNDGNTNFGSGNAGFLNIGSGNEGSGNLGFGNAGDDNTGWGNSGDTNTGGFNSGDLNTGIGSPVTQGVANSGFGNTGTGHSGFFNSGNSGSGFQNLGNGSSGFGNASDTSSGFQNAGTALTRASSTWADSPRAWPIRAPSRLQVWRTRATTARECSIRVIISRVSSTGAPPQKKVGNSG