Rv0278c Family assigned · medium auto-curated
H37Rv Rv0278c · MTBC0 - ·
957 aa · 333437–336310 (-) ·
RefSeq YP_177707.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PE-PGRS family protein PE_PGRS3 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PE-PGRS family protein PE_PGRS3. 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 |
P9WIG3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | PE-PGRS family protein PE_PGRS3 |
| Curated function | The arginine-rich C-terminal region protrudes from the mycobacterial membrane and mediates M.tuberculosis entry into host epithelial cells. May serve as a bridge between mycobacteria and host cells by interacting with specific host phospholipids and extracting them from host cells, for their direct integration or as a source of phosphate, during phases of TB pathogenesis when M.tuberculosis is short of phosphate supply. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | PE-PGRS family |
| Orthologous group | COG3391 |
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 | 0.293 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 21 synonymous, 15 missense, 0 nonsense, 4 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 7.68% of strains (11153) · convergent |
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 | 1.2e-33 | 4–94 | PE family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB25 (Rv0277A, len: 85 aa. Possible vapB25, antitoxin,part of toxin-antitoxin (TA) operon with Rv0277c, see Arcus et al. 2005. Has in-frame stop c), high confidence from genomic context alone (score 723 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0277A vapB25 |
Rv0277A, len: 85 aa. Possible vapB25, antitoxin,part of toxin-antitoxin (TA) operon with Rv0277c, see Arcus et al. 2005. Has in-frame stop c | 723 | 723 ctx | neighborhood:723 |
Rv0277c vapC25 |
ribonuclease VapC25 | 660 | 660 ctx | neighborhood:660 |
Rv0279c PE_PGRS4 |
PE-PGRS family protein PE_PGRS4 | 430 | 423 ctx | neighborhood:423 |
Rv0198c zmp1 |
zinc metalloprotease | 407 | 407 | |
Rv0931c pknD |
serine/threonine-protein kinase PknD | 413 | 210 | |
Rv1899c lppD |
lipoprotein LppD | 803 | 43 | textmining:803 |
Rv0311 hyp |
hypothetical protein | 579 | 43 | textmining:579 |
Rv0805 cpdA |
3',5'-cyclic adenosine monophosphate phosphodiesterase CpdA | 512 | 42 | textmining:512 |
Rv3426 PPE58 |
PPE family protein PPE58 | 803 | 41 | textmining:803 |
Rv3344c PE_PGRS49 |
PE-PGRS family protein PE_PGRS49 | 656 | 41 | textmining:656 |
Rv3159c PPE53 |
PPE family protein PPE53 | 652 | 41 | textmining:652 |
Rv0619 galTb |
Rv0619, (MTCY19H5.02c), len: 181 aa (probable partial CDS). Probable galTb, second part of galactose-1-phosphate uridylyltransferase, highly | 510 | 41 | textmining:510 |
Rv1267c embR |
transcriptional regulator EmbR | 439 | 41 | textmining:439 |
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-PGRS family protein PE_PGRS3
- Pfam (hmmscan --cut_ga): PE PF00934.26 (E=1e-33)
- (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_177707.1)
- 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
COG3391 - Curated reference: UniProt P9WIG3 (SwissProt, reviewed; Evidence at protein 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 —
13 functional partner(s); context anchor
vapB25 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0278c| MSFVIAAPEVIAAAATDLASLGSSISAANAAAAANTTALMAAGADEVSTAIAALFGAHGQAYQALSAQAQAFHAQFVQALTSGGGAYAAAEAAAVSPLLDPINEFFLANTGRPLIGNGANGAPGTGANGGDGGWLIGNGGAGGSGAAGVNGGAGGNGGAGGNGGAGGLIGNGGAGGAGGVASSGIGGSGGAGGNAMLFGAGGAGGAGGGVVALTGGAGGAGGAGGNAGLLFGAAGVGGAGGFTNGSALGGAGGAGGAGGLFATGGVGGSGGAGSSGGAGGAGGAGGLFGAGGTGGHGGFADSSFGGVGGAGGAGGLFGAGGEGGSGGHSLVAGGDGGAGGNAGMLALGAAGGAGGIGGDGGTLTAGGIGGAGGAGGNAGLLFGSGGSGGAGGFGFADGGQGGPGGNAGTVFGSGGAGGNGGVGQGFAGGIGGAGGTPGLIGNGGNGGNGGASAVTGGNGGIGGTGVLIGNGGNGGSGGIGAGKAGVGGVSGLLLGLDGFNAPASTSPLHTLQQNVLNVVNEPFQTLTGRPLIGNGANGTPGTGADGGAGGWLFGNGANGTPGTGAAGGAGGWLFGNGGNGGHGATNTAATATGGAGGAGGILFGTGGNGGTGGIATGAGGIGGAGGAGGVSLLIGSGGTGGNGGNSIGVAGIGGAGGRGGDAGLLFGAAGTGGHGAAGGVPAGVGGAGGNGGLFANGGAGGAGGFNAAGGNGGNGGLFGTGGTGGAGTNFGAGGNGGNGGLFGAGGTGGAAGSGGSGITTGGGGHGGNAGLLSLGASGGAGGSGGASSLAGGAGGTGGNGALLFGFRGAGGAGGHGGAALTSIQQGGAGGAGGNGGLLFGSAGAGGAGGSGANALGAGTGGTGGDGGHAGVFGNGGDGGCRRVWRRYRRQRWCRRQRRADRQRRQRRQRRQSRGHARCRRHRRAAARRERTQRLAIAGRPATTRGVEGISCSPQMMP