espK Family assigned · medium auto-curated
H37Rv Rv3879c · MTBC0 - ·
729 aa · 4357593–4359782 (-) ·
RefSeq NP_218396.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-1 secretion-associated protein EspK |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | ESX-1 secretion-associated protein EspK. Pfam: EspK_C (PF27215.1). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WJC1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESX-1 secretion-associated protein EspK |
| Curated function | May act as a chaperone that facilitates EspB secretion through an interaction with EccCb1. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | espK |
| eggNOG description | domain protein |
| Orthologous group | COG4932 |
| Gene Ontology (11) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0016020, GO:0044424, GO:0044444, 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 | 0.443 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 14 synonymous, 17 missense, 0 nonsense, 10 frameshift |
| Disruption | 10 distinct premature-stop/frameshift site(s); most common in 2.33% of strains (3385) · 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 |
|---|---|---|---|---|
EspK_C | PF27215.1 | 3.5e-108 | 502–725 | EspK C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccE1 (ESX-1 secretion system protein EccE1), high confidence from genomic context alone (score 825 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3881c espB |
ESX-1 secretion-associated protein EspB | 989 | 912 | experimental:900 textmining:886 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 937 | 825 ctx | cooccurence:768 textmining:659 |
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 929 | 802 ctx | cooccurence:768 textmining:657 |
Rv0341 iniB |
isoniazid inducible protein IniB | 774 | 775 ctx | cooccurence:774 |
Rv0355c PPE8 |
PPE family protein PPE8 | 773 | 773 ctx | cooccurence:773 |
Rv3350c PPE56 |
PPE family protein PPE56 | 773 | 773 ctx | cooccurence:773 |
Rv1004c |
membrane protein | 773 | 773 ctx | cooccurence:773 |
Rv3347c PPE55 |
PPE family protein PPE55 | 773 | 773 ctx | cooccurence:773 |
Rv0304c PPE5 |
PPE family protein PPE5 | 773 | 773 ctx | cooccurence:773 |
Rv1917c PPE34 |
PPE family protein PPE34 | 773 | 773 ctx | cooccurence:773 |
Rv3864 espE |
ESX-1 secretion-associated protein EspE | 830 | 772 ctx | cooccurence:772 |
Rv3343c PPE54 |
PPE family protein PPE54 | 777 | 772 ctx | cooccurence:772 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 772 | 772 ctx | cooccurence:772 |
Rv2209 |
integral membrane protein | 772 | 772 ctx | cooccurence:772 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 772 | 772 ctx | cooccurence:772 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): ESX-1 secretion-associated protein EspK
- Pfam (hmmscan --cut_ga): EspK_C PF27215.1 (E=3e-108)
- (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_218396.1)
- Domains: Pfam-A via hmmscan --cut_ga — EspK_C (PF27215.1)
- 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
COG4932 - Curated reference: UniProt P9WJC1 (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 —
155 functional partner(s); context anchor
eccE1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3879c|espK MSITRPTGSYARQMLDPGGWVEADEDTFYDRAQEYSQVLQRVTDVLDTCRQQKGHVFEGGLWSGGAANAANGALGANINQLMTLQDYLATVITWHRHIAGLIEQAKSDIGNNVDGAQREIDILENDPSLDADERHTAINSLVTATHGANVSLVAETAERVLESKNWKPPKNALEDLLQQKSPPPPDVPTLVVPSPGTPGTPGTPITPGTPITPGTPITPIPGAPVTPITPTPGTPVTPVTPGKPVTPVTPVKPGTPGEPTPITPVTPPVAPATPATPATPVTPAPAPHPQPAPAPAPSPGPQPVTPATPGPSGPATPGTPGGEPAPHVKPAALAEQPGVPGQHAGGGTQSGPAHADESAASVTPAAASGVPGARAAAAAPSGTAVGAGARSSVGTAAASGAGSHAATGRAPVATSDKAAAPSTRAASARTAPPARPPSTDHIDKPDRSESADDGTPVSMIPVSAARAARDAATAAASARQRGRGDALRLARRIAAALNASDNNAGDYGFFWITAVTTDGSIVVANSYGLAYIPDGMELPNKVYLASADHAIPVDEIARCATYPVLAVQAWAAFHDMTLRAVIGTAEQLASSDPGVAKIVLEPDDIPESGKMTGRSRLEVVDPSAAAQLADTTDQRLLDLLPPAPVDVNPPGDERHMLWFELMKPMTSTATGREAAHLRAFRAYAAHSQEIALHQAHTATDAAVQRVAVADWLYWQYVTGLLDRALAAAC