eccE3 Family assigned · medium auto-curated
H37Rv Rv0292 · MTBC0 mtbc0_000311 ·
331 aa · 359174–360169 (+) ·
RefSeq NP_214806.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-3 secretion system protein EccE |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-3 subunit EccE3 |
| Revised (this work) | Type VII secretion system ESX-3 subunit EccE3. 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 |
P9WJE5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESX-3 secretion system protein EccE3 |
| Curated function | Part of the ESX-3 specialized secretion system, which is important for iron and zinc uptake or homeostasis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | eccE3 |
| eggNOG description | Putative type VII ESX secretion system translocon, EccE |
| Orthologous group | 2AP0J |
| Gene Ontology (16) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0005887, GO:0008150, GO:0016020, GO:0016021, GO:0030312, GO:0031224, GO:0031226, GO:0040007 +4 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)
| pN/pS | 1.968 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 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 |
|---|---|---|---|---|
EccE | PF11203.14 | 1.0e-15 | 127–214 | Putative type VII ESX secretion system translocon, EccE |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccD3 (ESX-3 secretion system protein EccD), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 999 | 1000 ctx | neighborhood:882 coexpression:860 experimental:997 textmining:953 |
Rv0284 eccC3 |
ESX-3 secretion system protein EccC3 | 999 | 986 ctx | neighborhood:584 coexpression:757 experimental:870 textmining:958 |
Rv0291 mycP3 |
membrane-anchored mycosin MycP | 991 | 983 ctx | neighborhood:882 coexpression:860 textmining:541 |
Rv0283 eccB3 |
ESX-3 secretion system protein EccB3 | 999 | 982 ctx | neighborhood:538 coexpression:729 experimental:870 textmining:959 |
Rv0289 espG3 |
ESX-3 secretion-associated protein EspG3 | 988 | 966 ctx | neighborhood:815 coexpression:822 textmining:678 |
Rv0286 PPE4 |
PPE family protein PPE4 | 933 | 904 ctx | neighborhood:457 coexpression:831 |
Rv3448 eccD4 |
ESX-4 secretion system protein EccD4 | 850 | 841 | experimental:830 |
Rv1782 eccB5 |
ESX-5 type VII secretion system protein EccB5 | 921 | 781 | experimental:767 textmining:654 |
Rv0288 esxH |
ESAT-6-like protein EsxH | 835 | 711 ctx | neighborhood:658 textmining:451 |
Rv0287 esxG |
ESAT-6 like protein EsxG | 824 | 685 ctx | neighborhood:592 textmining:467 |
Rv0282 eccA3 |
ESX-3 secretion system protein EccA | 965 | 668 ctx | neighborhood:583 textmining:901 |
Rv1783 eccC5 |
ESX-5 type VII secretion system protein EccC5 | 629 | 575 | experimental:571 |
Rv3894c eccC2 |
ESX-2 type VII secretion system protein EccC | 629 | 575 | experimental:571 |
Rv3447c eccC4 |
ESX-4 secretion system protein EccC4 | 628 | 574 | experimental:571 |
Rv0285 PE5 |
PE family protein PE5 | 560 | 509 ctx | neighborhood:509 |
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-3 secretion system protein EccE
- MTBC0 PGAP product: type VII secretion system ESX-3 subunit EccE3
- Pfam (hmmscan --cut_ga): EccE PF11203.14 (E=1e-15)
- (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_214806.1)
- 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
2AP0J - Curated reference: UniProt P9WJE5 (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 —
35 functional partner(s); context anchor
eccD3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000311|Rv0292|eccE3 MNPIPSWPGRGRVTLVLLAVVPVALAYPWQSTRDYVLLGVAAAVVIGLFGFWRGLYFTTIARRGLAILRRRRRIAEPATCTRTTVLVWVGPPASDTNVLPLTLIARYLDRYGIRADTIRITSRVTASGDCRTWVGLTVVADDNLAALQARSARIPLQETAQVAARRLADHLREIGWEAGTAAPDEIPALVAADSRETWRGMRHTDSDYVAAYRVSADAELPDTLPAIRSRPAQETWIALEIAYAAGSSTRYTVAAACALRTDWRPGGTAPVAGLLPQHGNHVPALTALDPRSTRRLDGHTDAPADLLTRLHWPTPTAGAHRAPLTNAVSRT