espE Resolved · high auto-curated
H37Rv Rv3864 · MTBC0 mtbc0_004097 ·
418 aa · 4364379–4365635 (+) ·
RefSeq NP_218381.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-1 secretion-associated protein EspE |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-1 associated protein EspE |
| Revised (this work) | Type VII secretion system ESX-1 associated protein EspE. Pfam: EspA_EspE (PF18879.7). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJD3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESX-1 secretion-associated protein EspE |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | domain, Protein |
| Orthologous group | COG3266 |
| Gene Ontology (8) |
GO:0008150, GO:0040007, GO:0044110, GO:0044116, GO:0044117, GO:0044403, GO:0044419, GO:0051704
|
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 | 0.516 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 8 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 |
|---|---|---|---|---|
EspA_EspE | PF18879.7 | 2.1e-23 | 22–104 | EspA/EspE family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: espG1 (ESX-1 secretion-associated protein EspG), high confidence from genomic context alone (score 935 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3866 espG1 |
ESX-1 secretion-associated protein EspG | 946 | 935 ctx | neighborhood:594 coexpression:846 |
Rv3876 espI |
ESX-1 secretion-associated protein EspI | 941 | 884 ctx | cooccurence:436 coexpression:774 textmining:518 |
Rv3873 PPE68 |
PPE family protein PPE68 | 894 | 883 | coexpression:850 |
Rv1917c PPE34 |
PPE family protein PPE34 | 776 | 777 ctx | cooccurence:771 |
Rv3350c PPE56 |
PPE family protein PPE56 | 780 | 776 ctx | cooccurence:773 |
Rv3347c PPE55 |
PPE family protein PPE55 | 775 | 775 ctx | cooccurence:772 |
Rv0355c PPE8 |
PPE family protein PPE8 | 774 | 775 ctx | cooccurence:772 |
Rv0304c PPE5 |
PPE family protein PPE5 | 774 | 774 ctx | cooccurence:771 |
Rv3343c PPE54 |
PPE family protein PPE54 | 773 | 773 ctx | cooccurence:771 |
Rv3879c espK |
ESX-1 secretion-associated protein EspK | 830 | 772 ctx | cooccurence:772 |
Rv1004c |
membrane protein | 771 | 772 ctx | cooccurence:770 |
Rv0341 iniB |
isoniazid inducible protein IniB | 776 | 771 ctx | cooccurence:770 |
Rv0755c PPE12 |
PPE family protein PPE12 | 771 | 771 ctx | cooccurence:768 |
Rv2082 hyp |
hypothetical protein | 778 | 770 ctx | cooccurence:760 |
Rv1753c PPE24 |
PPE family protein PPE24 | 770 | 770 ctx | cooccurence:768 |
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 EspE
- MTBC0 PGAP product: type VII secretion system ESX-1 associated protein EspE
- Pfam (hmmscan --cut_ga): EspA_EspE PF18879.7 (E=2e-23)
- (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_218381.1)
- Domains: Pfam-A via hmmscan --cut_ga — EspA_EspE (PF18879.7)
- 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
COG3266 - Curated reference: UniProt P9WJD3 (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 —
138 functional partner(s); context anchor
espG1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004097|Rv3864|espE MASGSGLCKTTSNFIWGQLLLLGEGIPDPGDIFNTGSSLFKQISDKMGLAIPGTNWIGQAAEAYLNQNIAQQLRAQVMGDLDKLTGNMISNQAKYVSDTRDVLRAMKKMIDGVYKVCKGLEKIPLLGHLWSWELAIPMSGIAMAVVGGALLYLTIMTLMNATNLRGILGRLIEMLTTLPKFPGLPGLPSLPDIIDGLWPPKLPDIPIPGLPDIPGLPDFKWPPTPGSPLFPDLPSFPGFPGFPSLPGFPGLPGFPEFPAIPGFPALPGLPSIPNLFPGLPGLGDLLPGVGDLGKLPTWTELAALPDFLGGFAGLPSLGFGNLLSFASLPTVGQVTATMGQLQQLVAAGGGPSQLASMGSQQAQLISSQAQQGGQQHATLVSDKKEDEEGAAAGVAEAERAPIDAGTAASQRGQEGTVL