PPE7 Family assigned · low auto-curated
H37Rv Rv0354c · MTBC0 - ·
141 aa · 424269–424694 (-) ·
RefSeq YP_177720.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PPE family protein PPE7 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PPE family protein PPE7. |
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 |
L0T545
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | PPE family protein PPE7 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
U Intracellular trafficking, secretion and vesicular transport
|
|---|---|
| eggNOG description | domain, Protein |
| Orthologous group | COG3210 |
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 | 0.136 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 2 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 99.20% of strains (144053) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PPE8 (PPE family protein PPE8), medium confidence from genomic context alone (score 575 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0355c PPE8 |
PPE family protein PPE8 | 579 | 575 ctx | neighborhood:553 |
Rv0357c purA |
adenylosuccinate synthetase | 429 | 358 | |
Rv2353c PPE39 |
PPE family protein PPE39 | 517 | 54 | textmining:511 |
Rv0878c PPE13 |
PPE family protein PPE13 | 517 | 53 | textmining:511 |
Rv2345 |
transmembrane protein | 512 | 44 | textmining:511 |
Rv3738c PPE66 |
PPE family protein PPE66 | 435 | 44 | textmining:434 |
Rv3426 PPE58 |
PPE family protein PPE58 | 408 | 44 | textmining:407 |
Rv2371 PE_PGRS40 |
PE-PGRS family protein PE_PGRS40 | 546 | 41 | textmining:546 |
Rv0297 PE_PGRS5 |
PE-PGRS family protein PE_PGRS5 | 527 | 41 | textmining:528 |
Rv3595c PE_PGRS59 |
PE-PGRS family protein PE_PGRS59 | 511 | 41 | textmining:511 |
Rv2408 PE24 |
PE family protein PE24 | 434 | 41 | textmining:434 |
Rv0388c PPE9 |
Rv0388c, (MTV036.23c), len: 180 aa. PPE9, Member of the Mycobacterium tuberculosis PPE family, highly similar to others e.g. MTCY10G2_10|Z92 | 432 | 41 | textmining:432 |
Rv1768 PE_PGRS31 |
PE-PGRS family protein PE_PGRS31 | 431 | 41 | textmining:431 |
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 PPE7
- (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_177720.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG3210 - Curated reference: UniProt L0T545 (TrEMBL, unreviewed; Predicted)
- 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 —
13 functional partner(s); context anchor
PPE8 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0354c|PPE7 MSVCVIYIPFKGCVKHVSVTIPITTEHLGPYEIDASTINPDQPIDTAFTQTLDFAGSGTVGAFPFGFGWQQSPGFFNSTTTPSSGFFNSGAGGASGFLNDAAAAVSGLGNVFTETSGFFNAGGVGIRASKTSATCCRAGRT