PPE23 Family assigned · medium auto-curated
H37Rv Rv1706c · MTBC0 - ·
394 aa · 1932694–1933878 (-) ·
RefSeq YP_177828.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PPE family protein PPE23 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PPE family protein PPE23. 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 |
E2FZM4
SwissProt · reviewed
· Evidence at transcript level
|
|---|---|
| UniProt name | Uncharacterized protein SocA |
UniProt still lists this protein as Uncharacterized protein SocA; 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 |
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 | 0.831 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 7 missense, 0 nonsense, 0 frameshift |
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 | 2.7e-66 | 38–198 | PPE family |
PPE-SVP | PF12484.14 | 3.2e-11 | 312–388 | PPE-SVP subfamily C-terminal region |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PPE22 (PPE family protein PPE22), medium confidence from genomic context alone (score 695 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1705c PPE22 |
PPE family protein PPE22 | 721 | 695 ctx | neighborhood:675 |
Rv1704c cycA |
D-serine/alanine/glycine transporter protein CycA | 566 | 566 ctx | neighborhood:564 |
Rv1703c |
methyltransferase | 444 | 445 ctx | neighborhood:443 |
Rv1706A hyp |
hypothetical protein | 871 | 50 | textmining:870 |
Rv3095 |
HTH-type transcriptional regulator | 655 | 47 | textmining:653 |
Rv1862 adhA |
alcohol dehydrogenase A | 653 | 47 | textmining:651 |
Rv3047c hyp |
hypothetical protein | 659 | 46 | textmining:658 |
Rv2325c hyp |
hypothetical protein | 659 | 45 | textmining:658 |
Rv1147 hyp |
hypothetical protein | 661 | 44 | textmining:660 |
Rv2303c |
antibiotic-resistance protein | 631 | 44 | textmining:630 |
Rv1352 hyp |
hypothetical protein | 627 | 44 | textmining:626 |
Rv1341 rdgB |
non-canonical purine NTP pyrophosphatase | 549 | 44 | textmining:548 |
Rv0187 |
O-methyltransferase | 547 | 43 | textmining:547 |
Rv1867 hyp |
hypothetical protein | 437 | 43 | textmining:436 |
Rv1382 hyp |
hypothetical protein | 627 | 42 | textmining:627 |
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 PPE23
- Pfam (hmmscan --cut_ga): PPE PF00823.26 (E=3e-66), PPE-SVP PF12484.14 (E=3e-11)
- (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_177828.1)
- 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 E2FZM4 (SwissProt, reviewed; Evidence at transcript level)
- 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 —
18 functional partner(s); context anchor
PPE22 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1706c|PPE23 MTLDVPVNQGHVPPGSVACCLVGVTAVADGIAGHSLSNFGALPPEINSGRMYSGPGSGPLMAAAAAWDGLAAELSSAATGYGAAISELTNMRWWSGPASDSMVAAVLPFVGWLSTTATLAEQAAMQARAAAAAFEAAFAMTVPPPAIAANRTLLMTLVDTNWFGQNTPAIATTESQYAEMWAQDAAAMYGYASAAAPATVLTPFAPPPQTTNATGLVGHATAVAALRGQHSWAAAIPWSDIQKYWMMFLGALATAEGFIYDSGGLTLNALQFVGGMLWSTALAEAGAAEAAAGAGGAAGWSAWSQLGAGPVAASATLAAKIGPMSVPPGWSAPPATPQAQTVARSIPGIRSAAEAAETSVLLRGAPTPGRSRAAHMGRRYGRRLTVMADRPNVG