esxF Resolved · high auto-curated
H37Rv Rv3905c · MTBC0 mtbc0_004139 ·
103 aa · 4414972–4415283 (-) ·
RefSeq NP_218422.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESAT-6 like protein EsxF |
|---|---|
| MTBC0 PGAP re-annotation | pore-forming CpnT exporter EsxF |
| Revised (this work) | Pore-forming CpnT exporter EsxF. 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 |
P9WNH7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESAT-6-like protein EsxF |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | esxF |
| eggNOG description | Belongs to the WXG100 family |
| Orthologous group | COG4842 |
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) pseudogene candidate
| pN/pS | 0.509 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 9.74% of strains (14144) · 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 | 7.3e-19 | 7–90 | Proteins of 100 residues with WXG |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: esxE (ESAT-6 like protein EsxE), high confidence from genomic context alone (score 922 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3904c esxE |
ESAT-6 like protein EsxE | 992 | 922 ctx | neighborhood:880 textmining:907 |
Rv3903c cpnT hyp |
hypothetical protein | 981 | 900 ctx | neighborhood:880 textmining:825 |
Rv3902c ift hyp |
hypothetical protein | 953 | 881 ctx | neighborhood:880 textmining:630 |
Rv3906c hyp |
hypothetical protein | 971 | 645 ctx | neighborhood:633 textmining:923 |
Rv3907c pcnA |
poly(A) polymerase PcnA | 588 | 589 ctx | neighborhood:586 |
Rv0287 esxG |
ESAT-6 like protein EsxG | 419 | 394 | |
Rv3020c esxS |
ESAT-6 like protein EsxS | 416 | 390 | |
Rv3447c eccC4 |
ESX-4 secretion system protein EccC4 | 414 | 378 | |
Rv3894c eccC2 |
ESX-2 type VII secretion system protein EccC | 409 | 372 | |
Rv2748c ftsK |
DNA translocase FtsK | 417 | 351 | |
Rv3911 sigM |
ECF RNA polymerase sigma factor SigM | 592 | 267 | textmining:466 |
Rv3444c esxT |
ESAT-6 like protein EsxT | 452 | 119 | textmining:405 |
Rv3875 esxA |
ESAT-6 protein EsxA | 404 | 107 | |
Rv3445c esxU |
ESAT-6 like protein EsxU | 517 | 101 | textmining:486 |
Rv3874 esxB |
ESAT-6-like protein EsxB | 487 | 83 | textmining:465 |
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 EsxF
- MTBC0 PGAP product: pore-forming CpnT exporter EsxF
- Pfam (hmmscan --cut_ga): WXG100 PF06013.19 (E=7e-19)
- (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_218422.1)
- 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 P9WNH7 (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 —
22 functional partner(s); context anchor
esxE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004139|Rv3905c|esxF MGADDTLRVEPAVMQGFAASLDGAAEHLAVQLAELDAQVGQMLGGWRGASGSAYGSAWELWHRGAGEVQLGLSMLAAAIAHAGAGYQHNETASAQVLREVGGG