PPE43 Family assigned · medium auto-curated
H37Rv Rv2768c · MTBC0 - ·
394 aa · 3076894–3078078 (-) ·
RefSeq YP_177906.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PPE family protein PPE43 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PPE family protein PPE43. Pfam: PPE (PF00823.26), PPE-SVP (PF12484.14). |
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 |
Q79FA9
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | PPE family protein PPE43 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
N Cell motility
|
|---|---|
| eggNOG description | Polymorphic PE/PPE proteins C terminal |
| Orthologous group | COG5651 |
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 | 1.823 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.45% of strains (650) · 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 |
|---|---|---|---|---|
PPE | PF00823.26 | 1.7e-62 | 2–164 | PPE family |
PPE-SVP | PF12484.14 | 1.3e-19 | 311–390 | PPE-SVP subfamily C-terminal region |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2767c (membrane protein), high confidence from genomic context alone (score 891 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1040c PE8 |
PE family protein PE8 | 907 | 899 | experimental:891 |
Rv1794 espG5 hyp |
hypothetical protein | 891 | 892 | experimental:891 |
Rv2767c |
membrane protein | 922 | 891 ctx | neighborhood:475 coexpression:800 |
Rv2769c PE27 |
PE family protein PE27 | 796 | 593 ctx | neighborhood:593 textmining:521 |
Rv2766c |
short-chain type dehydrogenase/reductase | 494 | 494 ctx | neighborhood:475 |
Rv0115 hddA |
D-alpha-D-heptose-7-phosphate kinase HddA | 659 | 54 | textmining:655 |
Rv2588c yajC |
membrane protein secretion factor YajC | 698 | 47 | textmining:697 |
Rv2589 gabT |
4-aminobutyrate aminotransferase | 860 | 46 | textmining:860 |
Rv3778c |
aminotransferase | 728 | 44 | textmining:728 |
Rv1535 hyp |
hypothetical protein | 657 | 41 | textmining:657 |
Rv3477 PE31 |
PE family protein PE31 | 528 | 41 | textmining:528 |
Rv0116c ldtA |
L,D-transpeptidase LdtA | 511 | 41 | textmining:511 |
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 PPE43
- Pfam (hmmscan --cut_ga): PPE PF00823.26 (E=2e-62), PPE-SVP PF12484.14 (E=1e-19)
- (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_177906.1)
- Domains: Pfam-A via hmmscan --cut_ga — PPE (PF00823.26), PPE-SVP (PF12484.14)
- 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 Q79FA9 (TrEMBL, unreviewed; 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 —
12 functional partner(s); context anchor
Rv2767c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2768c|PPE43 MDFGALPPEINSTRMYAGAGAAPLMAAGATWNGLAVELSTTASSVESVIMQLTTEQWLGPASMSMVVAAQPYLAWLTYTAESAAHAAAQAMASAAAFEAAFAMTVPPAEVAANRALLAALVATNVLGQNTPAIMATEAHYGEMWAQDALAMYGYAASSAAAGRLNPLITPSQTANMAGLAGQAAAVSHAAAASTVQQVGLGSLISNLPNAVMGFASPLTSAADAAGLGGIIQDIEELLGITFVQNAINGAVNTTAWFVMATIPNAVFLGHAFAALNPATVTAAADAVPAAAAAAGLAHTVTPVGVGGASLTASLGEASSVGGLSVPAGWSTAAPAMTSGTTALEGSGWAVPEEAGPVAAMPGMAGISGAAKGAGAYAGPRYGFKPIVMPKQVVV