espF Resolved · high auto-curated
H37Rv Rv3865 · MTBC0 mtbc0_004098 ·
103 aa · 4365723–4366034 (+) ·
RefSeq NP_218382.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-1 secretion-associated protein EspF |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-1 associated protein EspF |
| Revised (this work) | Type VII secretion system ESX-1 associated protein EspF. Pfam: T7SS_ESX_EspC (PF10824.15). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJD1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESX-1 secretion-associated protein EspF |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Excreted virulence factor EspC, type VII ESX diderm |
| Orthologous group | 2AGD7 |
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, GO:0044464, GO:0071944
|
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, 2 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 |
|---|---|---|---|---|
T7SS_ESX_EspC | PF10824.15 | 2.8e-28 | 1–100 | Excreted virulence factor EspC, type VII ESX diderm |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: espG1 (ESX-1 secretion-associated protein EspG), high confidence from genomic context alone (score 886 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3866 espG1 |
ESX-1 secretion-associated protein EspG | 937 | 886 ctx | neighborhood:881 textmining:469 |
Rv3868 eccA1 |
ESX-1 secretion system protein EccA1 | 938 | 833 ctx | neighborhood:825 textmining:650 |
Rv3870 eccCa1 |
ESX-1 secretion system protein EccCa | 832 | 833 ctx | neighborhood:825 |
Rv3869 eccB1 |
ESX-1 secretion system protein EccB | 897 | 827 ctx | neighborhood:825 textmining:431 |
Rv3871 eccCb1 |
ESX-1 secretion system protein EccCb | 752 | 748 ctx | neighborhood:736 |
Rv3867 espH |
ESX-1 secretion-associated protein EspH | 924 | 704 ctx | neighborhood:687 textmining:755 |
Rv3864 espE |
ESX-1 secretion-associated protein EspE | 873 | 624 ctx | neighborhood:600 textmining:677 |
Rv3863 hyp |
hypothetical protein | 800 | 408 ctx | neighborhood:402 textmining:677 |
Rv3873 PPE68 |
PPE family protein PPE68 | 569 | 373 | |
Rv3874 esxB |
ESAT-6-like protein EsxB | 783 | 289 | textmining:707 |
Rv3875 esxA |
ESAT-6 protein EsxA | 490 | 251 | |
Rv3881c espB |
ESX-1 secretion-associated protein EspB | 733 | 233 | textmining:667 |
Rv3878 espJ |
ESX-1 secretion-associated protein EspJ | 610 | 178 | textmining:545 |
Rv3614c espD |
ESX-1 secretion-associated protein EspD | 584 | 160 | textmining:525 |
Rv3616c espA |
ESX-1 secretion-associated protein EspA | 543 | 126 | textmining:500 |
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: ESX-1 secretion-associated protein EspF
- MTBC0 PGAP product: type VII secretion system ESX-1 associated protein EspF
- Pfam (hmmscan --cut_ga): T7SS_ESX_EspC PF10824.15 (E=3e-28)
- (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_218382.1)
- Domains: Pfam-A via hmmscan --cut_ga — T7SS_ESX_EspC (PF10824.15)
- 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
2AGD7 - Curated reference: UniProt P9WJD1 (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
espG1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004098|Rv3865|espF MTGFLGVVPSFLKVLAGMHNEIVGDIKRATDTVAGISGRVQLTHGSFTSKFNDTLQEFETTRSSTGTGLQGVTSGLANNLLAAAGAYLKADDGLAGVIDKIFG