esxR Family assigned · medium auto-curated
H37Rv Rv3019c · MTBC0 mtbc0_003210 ·
96 aa · 3400020–3400310 (-) ·
RefSeq NP_217535.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESAT-6 like protein EsxR |
|---|---|
| MTBC0 PGAP re-annotation | WXG100 family type VII secretion target |
| Revised (this work) | WXG100 family type VII secretion target. Pfam: WXG100 (PF06013.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNI9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESAT-6-like protein EsxR |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | esxH |
| eggNOG description | Belongs to the WXG100 family |
| Orthologous group | COG4842 |
| Gene Ontology (2) |
GO:0005575, GO:0032991
|
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, 1 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.84% of strains (1219) · clonal |
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 |
|---|---|---|---|---|
WXG100 | PF06013.19 | 9.6e-19 | 3–87 | Proteins of 100 residues with WXG |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: esxS (ESAT-6 like protein EsxS), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3020c esxS |
ESAT-6 like protein EsxS | 999 | 1000 ctx | neighborhood:682 coexpression:733 experimental:999 textmining:861 |
Rv0287 esxG |
ESAT-6 like protein EsxG | 956 | 833 | experimental:822 textmining:751 |
Rv3018c PPE46 |
PPE family protein PPE46 | 635 | 453 | |
Rv3350c PPE56 |
PPE family protein PPE56 | 431 | 431 | coexpression:431 |
Rv3018A PE27A |
Rv3018A, len: 28 aa. PE27A, Member of Mycobacterium tuberculosis PE family (see Brennan and Delogu, 2002), most similar to Rv0285 (102 aa), | 652 | 407 ctx | neighborhood:407 textmining:437 |
Rv0284 eccC3 |
ESX-3 secretion system protein EccC3 | 456 | 406 | |
Rv3894c eccC2 |
ESX-2 type VII secretion system protein EccC | 483 | 349 | |
Rv0289 espG3 |
ESX-3 secretion-associated protein EspG3 | 518 | 145 | textmining:460 |
Rv3022A PE29 |
PE family protein PE29 | 433 | 93 | textmining:401 |
Rv1917c PPE34 |
PPE family protein PPE34 | 440 | 50 | textmining:435 |
Rv1304 atpB |
ATP synthase subunit A | 474 | 47 | textmining:471 |
Rv3875 esxA |
ESAT-6 protein EsxA | 693 | 44 | textmining:692 |
Rv3874 esxB |
ESAT-6-like protein EsxB | 605 | 44 | textmining:605 |
Rv0294 tam |
trans-aconitate methyltransferase | 541 | 44 | textmining:540 |
Rv1038c esxJ |
ESAT-6 like protein EsxJ | 540 | 44 | textmining:539 |
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
- Legacy H37Rv annotation: ESAT-6 like protein EsxR
- MTBC0 PGAP product: WXG100 family type VII secretion target
- Pfam (hmmscan --cut_ga): WXG100 PF06013.19 (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 NP_217535.1)
- Domains: Pfam-A via hmmscan --cut_ga — WXG100 (PF06013.19)
- 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
COG4842 - Curated reference: UniProt P9WNI9 (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 —
19 functional partner(s); context anchor
esxS - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003210|Rv3019c|esxR MSQIMYNYPAMMAHAGDMAGYAGTLQSLGADIASEQAVLSSAWQGDTGITYQGWQTQWNQALEDLVRAYQSMSGTHESNTMAMLARDGAEAAKWGG