PE29 Family assigned · medium auto-curated
H37Rv Rv3022A · MTBC0 - ·
104 aa · 3380679–3380993 (-) ·
RefSeq YP_177685.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PE family protein PE29 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PE family protein PE29. Pfam: PE (PF00934.26). |
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 |
Q6MX17
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | PE family protein PE29 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Cell motility protein |
| Orthologous group | 2B7DA |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 3 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 |
|---|---|---|---|---|
PE | PF00934.26 | 1.5e-18 | 3–92 | PE family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PPE48 (Rv3021c, (MTV012.35c), len: 358 aa. PPE47, Member of Mycobacterium tuberculosis PPE family. Should be continuation of upstream ORF MTV012.36), high confidence from genomic context alone (score 798 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3022c PPE48 |
Rv3021c, (MTV012.35c), len: 358 aa. PPE47, Member of Mycobacterium tuberculosis PPE family. Should be continuation of upstream ORF MTV012.36 | 867 | 798 ctx | neighborhood:798 |
Rv3018c PPE46 |
PPE family protein PPE46 | 513 | 161 | textmining:444 |
Rv3020c esxS |
ESAT-6 like protein EsxS | 562 | 105 | textmining:532 |
Rv3017c esxQ |
ESAT-6 like protein EsxQ | 591 | 93 | textmining:568 |
Rv3019c esxR |
ESAT-6 like protein EsxR | 433 | 93 | textmining:401 |
Rv3739c PPE67 |
PPE family protein PPE67 | 560 | 71 | textmining:546 |
Rv2554c ruvX |
Holliday junction resolvase | 698 | 41 | textmining:698 |
Rv2555c alaS |
alanine--tRNA ligase | 680 | 41 | textmining:680 |
Rv1806 PE20 |
PE family protein PE20 | 572 | 41 | textmining:572 |
Rv1224 tatB |
Sec-independent protein translocase protein TatB | 545 | 41 | textmining:545 |
Rv3018A PE27A |
Rv3018A, len: 28 aa. PE27A, Member of Mycobacterium tuberculosis PE family (see Brennan and Delogu, 2002), most similar to Rv0285 (102 aa), | 543 | 41 | textmining:543 |
Rv3737 |
transmembrane protein | 449 | 41 | textmining:449 |
Rv2313c hyp |
hypothetical protein | 446 | 41 | textmining:446 |
Rv2694c hyp |
hypothetical protein | 412 | 41 | textmining:412 |
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): PE family protein PE29
- Pfam (hmmscan --cut_ga): PE PF00934.26 (E=1e-18)
- (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_177685.1)
- Domains: Pfam-A via hmmscan --cut_ga — PE (PF00934.26)
- 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
2B7DA - Curated reference: UniProt Q6MX17 (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 —
14 functional partner(s); context anchor
PPE48 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3022A|PE29 MTLRVVPEGLAAASAAVEALTARLAAAHAGAAPAITAVVAPAADPVSLQSAVGFSALGSEHAAIAGEGVEELGRSGVAVGESGIGYAAGDAVAAATYLVSGGSL