espB Resolved · high auto-curated
H37Rv Rv3881c · MTBC0 mtbc0_004115 ·
460 aa · 4384789–4386171 (-) ·
RefSeq NP_218398.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-1 secretion-associated protein EspB |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-1 target EspB |
| Revised (this work) | Type VII secretion system ESX-1 target EspB. Pfam: EspB_PE (PF18625.8), EspB_PPE (PF21856.3). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJD9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESX-1 secretion-associated protein EspB |
| Curated function | Required for host-cell death and may support an EsxA-independent virulence function. Secreted processed form of EspB binds to phosphatidic acid and phosphatidylserine. Inhibits IFN-gamma-induced autophagy in murine macrophages. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Preferred name | espB |
|---|---|
| Orthologous group | 2F9DC |
| Gene Ontology (29) |
GO:0002790, GO:0003674, GO:0005488, GO:0005515, GO:0005575, GO:0005576, GO:0006810, GO:0008104, GO:0008150, GO:0009306, GO:0009405, GO:0009987 +17 more
|
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 | 1.571 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 14 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 4.93% of strains (7158) · 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 |
|---|---|---|---|---|
EspB_PE | PF18625.8 | 8.2e-32 | 12–88 | ESX-1 secreted protein B PE domain |
EspB_PPE | PF21856.3 | 7.8e-66 | 130–281 | ESX-1 secretion-associated protein EspB, PPE domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: espL (ESX-1 secretion-associated protein EspL), high confidence from genomic context alone (score 978 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3880c espL |
ESX-1 secretion-associated protein EspL | 995 | 978 ctx | neighborhood:882 coexpression:822 textmining:817 |
Rv3879c espK |
ESX-1 secretion-associated protein EspK | 989 | 912 | experimental:900 textmining:886 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 923 | 772 ctx | neighborhood:769 textmining:676 |
Rv3883c mycP1 |
membrane-anchored mycosin | 950 | 745 ctx | neighborhood:731 textmining:812 |
Rv3864 espE |
ESX-1 secretion-associated protein EspE | 954 | 737 | coexpression:734 textmining:834 |
Rv3873 PPE68 |
PPE family protein PPE68 | 648 | 531 | coexpression:474 |
Rv1075c hyp |
hypothetical protein | 496 | 472 | experimental:425 |
Rv2418c octT hyp |
hypothetical protein | 495 | 471 | experimental:425 |
Rv0518 hyp |
hypothetical protein | 494 | 470 | experimental:425 |
Rv3866 espG1 |
ESX-1 secretion-associated protein EspG | 711 | 441 | coexpression:441 textmining:505 |
Rv1975 hyp |
hypothetical protein | 440 | 440 | coexpression:430 |
Rv0157A hyp |
hypothetical protein | 438 | 439 | coexpression:429 |
Rv0058 dnaB |
replicative DNA helicase | 449 | 427 | coexpression:407 |
Rv3867 espH |
ESX-1 secretion-associated protein EspH | 713 | 363 | textmining:568 |
Rv3878 espJ |
ESX-1 secretion-associated protein EspJ | 791 | 311 | textmining:710 |
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 EspB
- MTBC0 PGAP product: type VII secretion system ESX-1 target EspB
- Pfam (hmmscan --cut_ga): EspB_PE PF18625.8 (E=8e-32), EspB_PPE PF21856.3 (E=8e-66)
- (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_218398.1)
- Domains: Pfam-A via hmmscan --cut_ga — EspB_PE (PF18625.8), EspB_PPE (PF21856.3)
- 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
2F9DC - Curated reference: UniProt P9WJD9 (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 —
38 functional partner(s); context anchor
espL - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004115|Rv3881c|espB MTQSQTVTVDQQEILNRANEVEAPMADPPTDVPITPCELTAAKNAAQQLVLSADNMREYLAAGAKERQRLATSLRNAAKAYGEVDEEAATALDNDGEGTVQAESAGAVGGDSSAELTDTPRVATAGEPNFMDLKEAARKLETGDQGASLAHFADGWNTFNLTLQGDVKRFRGFDNWEGDAATACEASLDQQRQWILHMAKLSAAMAKQAQYVAQLHVWARREHPTYEDIVGLERLYAENPSARDQILPVYAEYQQRSEKVLTEYNNKAALEPVNPPKPPPAIKIDPPPPPQEQGLIPGFLMPPSDGSGVTPGTGMPAAPMVPPTGSPGGGLPADTAAQLTSAGREAAALSGDVAVKAASLGGGGGGGVPSAPLGSAIGGAESVRPAGAGDIAGLGQGRAGGGAALGGGGMGMPMGAAHQGQGGAKSKGSQQEDEALYTEDRAWTEAVIGNRRRQDSKESK