espJ Resolved · medium auto-curated
H37Rv Rv3878 · MTBC0 mtbc0_004112 ·
280 aa · 4380903–4381745 (+) ·
RefSeq NP_218395.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-1 secretion-associated protein EspJ |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-1 associated protein EspJ |
| Revised (this work) | Type VII secretion system ESX-1 associated protein EspJ. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJC3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESX-1 secretion-associated protein EspJ |
| Curated function | Could be involved in regulation of growth and intracellular survival. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2AWC2 |
|---|
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 | 0.538 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 8.88% of strains (12901) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: espI (ESX-1 secretion-associated protein EspI), high confidence from genomic context alone (score 824 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3876 espI |
ESX-1 secretion-associated protein EspI | 963 | 824 ctx | neighborhood:748 textmining:803 |
Rv3873 PPE68 |
PPE family protein PPE68 | 939 | 782 | coexpression:716 textmining:735 |
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 913 | 762 ctx | neighborhood:750 textmining:651 |
Rv3874 esxB |
ESAT-6-like protein EsxB | 920 | 609 | textmining:804 |
Rv3864 espE |
ESX-1 secretion-associated protein EspE | 648 | 549 | coexpression:411 |
Rv1364c |
sigma factor regulatory protein | 524 | 519 | coexpression:505 |
Rv3875 esxA |
ESAT-6 protein EsxA | 804 | 449 | textmining:659 |
Rv3866 espG1 |
ESX-1 secretion-associated protein EspG | 536 | 366 | |
Rv3869 eccB1 |
ESX-1 secretion system protein EccB | 450 | 315 | |
Rv3881c espB |
ESX-1 secretion-associated protein EspB | 791 | 311 | textmining:710 |
Rv3872 PE35 |
PE family protein PE35 | 745 | 223 | textmining:685 |
Rv3879c espK |
ESX-1 secretion-associated protein EspK | 894 | 222 | textmining:870 |
Rv3871 eccCb1 |
ESX-1 secretion system protein EccCb | 838 | 213 | textmining:803 |
Rv3868 eccA1 |
ESX-1 secretion system protein EccA1 | 616 | 210 | textmining:535 |
Rv3867 espH |
ESX-1 secretion-associated protein EspH | 540 | 206 | textmining:445 |
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 EspJ
- MTBC0 PGAP product: type VII secretion system ESX-1 associated protein EspJ
- (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_218395.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
2AWC2 - Curated reference: UniProt P9WJC3 (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 —
23 functional partner(s); context anchor
espI - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004112|Rv3878|espJ MAEPLAVDPTGLSAAAAKLAGLVFPQPPAPIAVSGTDSVVAAINETMPSIESLVSDGLPGVKAALTRTASNMNAAADVYAKTDQSLGTSLSQYAFGSSGEGLAGVASVGGQPSQATQLLSTPVSQVTTQLGETAAELAPRVVATVPQLVQLAPHAVQMSQNASPIAQTISQTAQQAAQSAQGGSGPMPAQLASAEKPATEQAEPVHEVTNDDQGDQGDVQPAEVVAAARDEGAGASPGQQPGGGVPAQAMDTGAGARPAASPLAAPVDPSTPAPSTTTTL