eccE1 Family assigned · medium auto-curated
H37Rv Rv3882c · MTBC0 mtbc0_004116 ·
462 aa · 4386278–4387666 (-) ·
RefSeq NP_218399.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-1 secretion system protein EccE1 |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-1 subunit EccE1 |
| Revised (this work) | Type VII secretion system ESX-1 subunit EccE1. 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 |
P9WJE9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESX-1 secretion system protein EccE1 |
| Curated function | Part of the ESX-1 specialized secretion system, which delivers several virulence factors to host cells during infection, including the key virulence factors EsxA (ESAT-6) and EsxB (CFP-10). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | eccE1 |
| eggNOG description | Putative type VII ESX secretion system translocon, EccE |
| Orthologous group | 2B6RE |
| 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 | 0.71 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 17 missense, 1 nonsense, 2 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 0.13% of strains (188) · 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 |
|---|---|---|---|---|
EccE | PF11203.14 | 5.2e-22 | 177–266 | Putative type VII ESX secretion system translocon, EccE |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mycP1 (membrane-anchored mycosin), high confidence from genomic context alone (score 987 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3883c mycP1 |
membrane-anchored mycosin | 996 | 987 ctx | neighborhood:882 cooccurence:503 coexpression:802 textmining:697 |
Rv3869 eccB1 |
ESX-1 secretion system protein EccB | 974 | 834 ctx | cooccurence:767 textmining:851 |
Rv3879c espK |
ESX-1 secretion-associated protein EspK | 937 | 825 ctx | cooccurence:768 textmining:659 |
Rv3870 eccCa1 |
ESX-1 secretion system protein EccCa | 926 | 805 ctx | cooccurence:699 textmining:640 |
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 933 | 784 ctx | cooccurence:774 textmining:704 |
Rv3881c espB |
ESX-1 secretion-associated protein EspB | 923 | 772 ctx | neighborhood:769 textmining:676 |
Rv3875 esxA |
ESAT-6 protein EsxA | 869 | 771 ctx | cooccurence:762 textmining:454 |
Rv3880c espL |
ESX-1 secretion-associated protein EspL | 889 | 766 ctx | neighborhood:763 textmining:547 |
Rv2542 hyp |
hypothetical protein | 790 | 760 ctx | cooccurence:758 |
Rv3884c eccA2 |
ESX-2 secretion system protein EccA | 801 | 739 ctx | neighborhood:731 |
Rv0341 iniB |
isoniazid inducible protein IniB | 720 | 721 ctx | cooccurence:720 |
Rv0658c |
integral membrane protein | 719 | 719 ctx | cooccurence:715 |
Rv1157c hyp |
hypothetical protein | 708 | 709 ctx | cooccurence:707 |
Rv1795 eccD5 |
ESX-5 type VII secretion system protein EccD | 794 | 674 | experimental:652 |
Rv3737 |
transmembrane protein | 668 | 668 ctx | cooccurence:668 |
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 system protein EccE1
- MTBC0 PGAP product: type VII secretion system ESX-1 subunit EccE1
- Pfam (hmmscan --cut_ga): EccE PF11203.14 (E=5e-22)
- (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_218399.1)
- 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
2B6RE - Curated reference: UniProt P9WJE9 (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 —
87 functional partner(s); context anchor
mycP1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004116|Rv3882c|eccE1 MRNPLGLRFSTGHALLASALAPPCIIAFLETRYWWAGIALASLGVIVATVTFYGRRITGWVAAVYAWLRRRRRPPDSSSEPVVGATVKPGDHVAVRWQGEFLVAVIELIPRPFTPTVIVDGQAHTDDMLDTGLVEELLSVHCPDLEADIVSAGYRVGNTAAPDVVSLYQQVIGTDPAPANRRTWIVLRADPERTRKSAQRRDEGVAGLARYLVASATRIADRLASHGVDAVCGRSFDDYDHATDIGFVREKWSMIKGRDAYTAAYAAPGGPDVWWSARADHTITRVRVAPGMAPQSTVLLTTADKPKTPRGFARLFGGQRPALQGQHLVANRHCQLPIGSAGVLVGETVNRCPVYMPFDDVDIALNLGDAQTFTQFVVRAAAAGAMVTVGPQFEEFARLIGAHIGQEVKVAWPNATTYLGPHPGIDRVILRHNVIGTPRHRQLPIRRVSPPEESRYQMALPK