espD Resolved · medium auto-curated
H37Rv Rv3614c · MTBC0 mtbc0_003831 ·
184 aa · 4077846–4078400 (-) ·
RefSeq NP_218131.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-1 secretion-associated protein EspD |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-1 target EspD |
| Revised (this work) | Type VII secretion system ESX-1 target EspD. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJD5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESX-1 secretion-associated protein EspD |
| Curated function | Required for ESX-1 function. Required for the maintenance of adequate cellular levels of both EspA and EspC. Facilitates EsxA secretion. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | interspecies interaction between organisms |
| Orthologous group | 2AVBJ |
| Gene Ontology (28) |
GO:0002790, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006810, GO:0008104, GO:0008150, GO:0009306, GO:0009987, GO:0015031, GO:0015833 +16 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 | 0.232 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 3 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: espC (ESX-1 secretion-associated protein EspC), high confidence from genomic context alone (score 935 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3615c espC |
ESX-1 secretion-associated protein EspC | 993 | 935 ctx | neighborhood:558 coexpression:860 textmining:908 |
Rv3616c espA |
ESX-1 secretion-associated protein EspA | 991 | 916 ctx | neighborhood:423 coexpression:860 textmining:902 |
Rv3613c hyp |
hypothetical protein | 912 | 912 ctx | neighborhood:574 coexpression:802 |
Rv3612c hyp |
hypothetical protein | 914 | 854 ctx | neighborhood:480 coexpression:730 textmining:440 |
Rv3880c espL |
ESX-1 secretion-associated protein EspL | 648 | 503 | experimental:500 |
Rv3871 eccCb1 |
ESX-1 secretion system protein EccCb | 416 | 166 | |
Rv3870 eccCa1 |
ESX-1 secretion system protein EccCa | 503 | 163 | textmining:431 |
Rv3868 eccA1 |
ESX-1 secretion system protein EccA1 | 436 | 163 | |
Rv3865 espF |
ESX-1 secretion-associated protein EspF | 584 | 160 | textmining:525 |
Rv3866 espG1 |
ESX-1 secretion-associated protein EspG | 505 | 159 | textmining:436 |
Rv3874 esxB |
ESAT-6-like protein EsxB | 718 | 156 | textmining:680 |
Rv3864 espE |
ESX-1 secretion-associated protein EspE | 654 | 152 | textmining:609 |
Rv3875 esxA |
ESAT-6 protein EsxA | 766 | 123 | textmining:744 |
Rv3824c papA1 |
acyltransferase | 417 | 68 | textmining:400 |
Rv3849 espR |
ESX-1 transcriptional regulator EspR | 637 | 55 | textmining:632 |
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 EspD
- MTBC0 PGAP product: type VII secretion system ESX-1 target EspD
- (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_218131.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
2AVBJ - Curated reference: UniProt P9WJD5 (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 —
21 functional partner(s); context anchor
espC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003831|Rv3614c|espD MDLPGNDFDSNDFDAVDLWGADGAEGWTADPIIGVGSAATPDTGPDLDNAHGQAETDTEQEIALFTVTNPPRTVSVSTLMDGRIDHVELSARVAWMSESQLASEILVIADLARQKAQSAQYAFILDRMSQQVDADEHRVALLRKTVGETWGLPSPEEAAAAEAEVFATRYSDDCPAPDDESDPW