PPE28 Family assigned · medium auto-curated
H37Rv Rv1800 · MTBC0 - ·
655 aa · 2039453–2041420 (+) ·
RefSeq YP_177839.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PPE family protein PPE28 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PPE family protein PPE28. Pfam: PPE (PF00823.26), PE-PPE (PF08237.18). |
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 |
P9WI11
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Uncharacterized PPE family protein PPE28 |
UniProt still lists this protein as Uncharacterized PPE family protein PPE28; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
N Cell motility
|
|---|---|
| eggNOG description | PE-PPE domain |
| 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 | 0.886 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 10 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.35% of strains (512) · 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 | 1.1e-59 | 4–167 | PPE family |
PE-PPE | PF08237.18 | 9.2e-87 | 245–469 | PE-PPE domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lppT (lipoprotein LppT), medium confidence from genomic context alone (score 623 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2108 PPE36 |
PPE family protein PPE36 | 742 | 738 | coexpression:738 |
Rv1799 lppT |
lipoprotein LppT | 623 | 623 ctx | neighborhood:529 |
Rv2431c PE25 |
PE family protein PE25 | 517 | 155 | textmining:453 |
Rv1147 hyp |
hypothetical protein | 520 | 55 | textmining:513 |
Rv1862 adhA |
alcohol dehydrogenase A | 442 | 54 | textmining:435 |
Rv3095 |
HTH-type transcriptional regulator | 442 | 47 | textmining:439 |
Rv1352 hyp |
hypothetical protein | 413 | 47 | textmining:410 |
Rv1756c |
Putative transposase; Rv1756c, (MTCY28.22c), len: 328 aa. Putative Transposase subunit for IS6110. Identical to many other M. tuberculosis I | 512 | 44 | textmining:511 |
Rv3893c PE36 |
PE family protein PE36 | 513 | 41 | textmining:513 |
Rv2303c |
antibiotic-resistance protein | 430 | 41 | textmining:430 |
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 PPE28
- Pfam (hmmscan --cut_ga): PPE PF00823.26 (E=1e-59), PE-PPE PF08237.18 (E=9e-87)
- (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_177839.1)
- Domains: Pfam-A via hmmscan --cut_ga — PPE (PF00823.26), PE-PPE (PF08237.18)
- 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 P9WI11 (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 —
10 functional partner(s); context anchor
lppT - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1800|PPE28 MLPNFAVLPPEVNSARVFAGAGSAPMLAAAAAWDDLASELHCAAMSFGSVTSGLVVGWWQGSASAAMVDAAASYIGWLSTSAAHAEGAAGLARAAVSVFEEALAATVHPAMVAANRAQVASLVASNLFGQNAPAIAALESLYECMWAQDAAAMAGYYVGASAVATQLASWLQRLQSIPGAASLDARLPSSAEAPMGVVRAVNSAIAANAAAAQTVGLVMGGSGTPIPSARYVELANALYMSGSVPGVIAQALFTPQGLYPVVVIKNLTFDSSVAQGAVILESAIRQQIAAGNNVTVFGYSQSATISSLVMANLAASADPPSPDELSFTLIGNPNNPNGGVATRFPGISFPSLGVTATGATPHNLYPTKIYTIEYDGVADFPRYPLNFVSTLNAIAGTYYVHSNYFILTPEQIDAAVPLTNTVGPTMTQYYIIRTENLPLLEPLRSVPIVGNPLANLVQPNLKVIVNLGYGDPAYGYSTSPPNVATPFGLFPEVSPVVIADALVAGTQQGIGDFAYDVSHLELPLPADGSTMPSTAPGSGTPVPPLSIDSLIDDLQVANRNLANTISKVAATSYATVLPTADIANAALTIVPSYNIHLFLEGIQQALKGDPMGLVNAVGYPLAADVALFTAAGGLQLLIIISAGRTIANDISAIVP