eccE2 Family assigned · medium auto-curated
H37Rv Rv3885c · MTBC0 mtbc0_004119 ·
537 aa · 4391154–4392767 (-) ·
RefSeq NP_218402.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-2 secretion system protein EccE |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-2 subunit EccE2 |
| Revised (this work) | Type VII secretion system ESX-2 subunit EccE2. Pfam: EccE (PF11203.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJE7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESX-2 secretion system protein EccE2 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Putative type VII ESX secretion system translocon, EccE |
| Orthologous group | 2BMYI |
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, 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 | 1.833 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 13 missense, 2 nonsense, 2 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 5.93% of strains (8606) · convergent |
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 |
|---|---|---|---|---|
EccE | PF11203.14 | 1.7e-18 | 173–262 | Putative type VII ESX secretion system translocon, EccE |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccA2 (ESX-2 secretion system protein EccA), high confidence from genomic context alone (score 954 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3884c eccA2 |
ESX-2 secretion system protein EccA | 954 | 954 ctx | neighborhood:794 coexpression:788 |
Rv3886c mycP2 |
membrane-anchored mycosin | 928 | 928 ctx | neighborhood:881 coexpression:423 |
Rv3888c |
membrane protein | 884 | 885 ctx | neighborhood:881 |
Rv3887c eccD2 |
ESX-2 secretion system protein EccD | 884 | 885 ctx | neighborhood:881 |
Rv3889c espG2 |
ESX-2 secretion-associated protein EspG2 | 597 | 597 ctx | neighborhood:593 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 525 | 525 ctx | neighborhood:503 |
Rv3883c mycP1 |
membrane-anchored mycosin | 468 | 467 ctx | neighborhood:459 |
Rv3890c esxC |
ESAT-6 like protein EsxC | 424 | 424 ctx | neighborhood:420 |
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-2 secretion system protein EccE
- MTBC0 PGAP product: type VII secretion system ESX-2 subunit EccE2
- Pfam (hmmscan --cut_ga): EccE PF11203.14 (E=2e-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_218402.1)
- Domains: Pfam-A via hmmscan --cut_ga — EccE (PF11203.14)
- 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
2BMYI - Curated reference: UniProt P9WJE7 (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 —
8 functional partner(s); context anchor
eccA2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004119|Rv3885c|eccE2 MTSKLTGFSPRSARRVAGVWTVFVLASAGWALGGQLGAVMAVVVGVALVFVQWWGQPAWSWAVLGLRGRRPVKWNDPITLANNRSGGGVRVQDGVAVVAVQLLGRAHRATTVTGSVTVESDNVIDVVELAPLLRHPLDLELDSISVVTFGSRTGTVGDYPRVYDAEIGTPPYAGRRETWLIMRLPVIGNTQALRWRTSVGAAAISVAQRVASSLRCQGLRAKLATATDLAELDRRLGSDAVAGSAQRWKAIRGEAGWMTTYAYPAEAISSRVLSQAWTLRADEVIQNVTVYPDATCTATITVRTPTPAPTPPSVILRRLNGEQAAAAAANMCGPRPHLRGQRRCPLPAQLVTEIGPSGVLIGKLSNGDRLMIPVTDAGELSRVFVAADDTIAKRIVIRVVGAGERVCVHTRDQERWASVRMPQLSIVGTPRPAPRTTVGVVEYVRRRKNGDDGKSEGSGVDVAISPTPRPASVITIARPGTSLSESDRHGFEVTIEQIDRATVKVGAAGQNWLVEMEMFRAENRYVSLEPVTMSIGR