PPE58 Family assigned · medium auto-curated
H37Rv Rv3426 · MTBC0 - ·
232 aa · 3843036–3843734 (+) ·
RefSeq YP_177972.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PPE family protein PPE58 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PPE family protein PPE58. Pfam: PPE (PF00823.26). |
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 |
Q50702
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Uncharacterized PPE family protein PPE58 |
UniProt still lists this protein as Uncharacterized PPE family protein PPE58; 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 (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 2.267 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 7 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 70.24% of strains (101996) · reference-fixed |
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 | 1.3e-38 | 1–126 | PPE family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PPE57 (PPE family protein PPE57), high confidence from genomic context alone (score 915 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3425 PPE57 |
PPE family protein PPE57 | 919 | 915 ctx | neighborhood:418 coexpression:860 |
Rv3429 PPE59 |
PPE family protein PPE59 | 742 | 730 | coexpression:730 |
Rv3159c PPE53 |
PPE family protein PPE53 | 533 | 86 | textmining:511 |
Rv3738c PPE66 |
PPE family protein PPE66 | 444 | 55 | textmining:436 |
Rv0305c PPE6 |
PPE family protein PPE6 | 443 | 50 | textmining:438 |
Rv0619 galTb |
Rv0619, (MTCY19H5.02c), len: 181 aa (probable partial CDS). Probable galTb, second part of galactose-1-phosphate uridylyltransferase, highly | 439 | 46 | textmining:437 |
Rv0805 cpdA |
3',5'-cyclic adenosine monophosphate phosphodiesterase CpdA | 438 | 44 | textmining:437 |
Rv0354c PPE7 |
PPE family protein PPE7 | 408 | 44 | textmining:407 |
Rv1899c lppD |
lipoprotein LppD | 758 | 42 | textmining:758 |
Rv0311 hyp |
hypothetical protein | 545 | 42 | textmining:545 |
Rv1267c embR |
transcriptional regulator EmbR | 433 | 42 | textmining:433 |
Rv1087 PE_PGRS21 |
PE-PGRS family protein PE_PGRS21 | 870 | 41 | textmining:870 |
Rv1067c PE_PGRS19 |
PE-PGRS family protein PE_PGRS19 | 805 | 41 | textmining:805 |
Rv0278c PE_PGRS3 |
PE-PGRS family protein PE_PGRS3 | 803 | 41 | textmining:803 |
Rv0747 PE_PGRS10 |
PE-PGRS family protein PE_PGRS10 | 728 | 41 | textmining:728 |
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 PPE58
- Pfam (hmmscan --cut_ga): PPE PF00823.26 (E=1e-38)
- (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_177972.1)
- Domains: Pfam-A via hmmscan --cut_ga — PPE (PF00823.26)
- 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
COG5651 - Curated reference: UniProt Q50702 (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 —
16 functional partner(s); context anchor
PPE57 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3426|PPE58 MHLMIPAEYISNVIYEGPRADSLYAADQRLRQLADSVRTTAESLNTTLDELHENWKGSSSEWMADAALRYLDWLSKHSRQILRTARVIESLVMAYEETLLRVVPPATIANNREEVRRLIASNVAGGKHSSNRRPRGTIRAVPGRKYPSNGPLSKLDPICAIEAAPMAGAAADPQERVGPRGRRGLAGQQQCRGRPGPSLRCSHDTPRFQMNQAFHTMVNMLLTCFACQEKPR