esxD Family assigned · medium auto-curated
H37Rv Rv3891c · MTBC0 mtbc0_004125 ·
107 aa · 4398295–4398618 (-) ·
RefSeq NP_218408.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESAT-6 like protein EsxD |
|---|---|
| MTBC0 PGAP re-annotation | WXG100 family type VII secretion target |
| Revised (this work) | WXG100 family type VII secretion target. Pfam: WXG100 (PF06013.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05453
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESAT-6-like protein EsxD |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | esxD |
| eggNOG description | Proteins of 100 residues with WXG |
| Orthologous group | 2A33T |
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) pseudogene candidate
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 9.86% of strains (14320) · 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 |
|---|---|---|---|---|
WXG100 | PF06013.19 | 3.4e-12 | 5–90 | Proteins of 100 residues with WXG |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: esxC (ESAT-6 like protein EsxC), high confidence from genomic context alone (score 757 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3890c esxC |
ESAT-6 like protein EsxC | 937 | 757 ctx | neighborhood:743 textmining:751 |
Rv3892c PPE69 |
PPE family protein PPE69 | 571 | 571 ctx | neighborhood:568 |
Rv3893c PE36 |
PE family protein PE36 | 501 | 501 ctx | neighborhood:501 |
Rv3889c espG2 |
ESX-2 secretion-associated protein EspG2 | 495 | 495 ctx | neighborhood:479 |
Rv0287 esxG |
ESAT-6 like protein EsxG | 441 | 51 | textmining:436 |
Rv1793 esxN |
ESAT-6 like protein EsxN | 403 | 50 | |
Rv1168c PPE17 |
PPE family protein PPE17 | 488 | 46 | textmining:486 |
Rv3445c esxU |
ESAT-6 like protein EsxU | 453 | 41 | textmining:454 |
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: ESAT-6 like protein EsxD
- MTBC0 PGAP product: WXG100 family type VII secretion target
- Pfam (hmmscan --cut_ga): WXG100 PF06013.19 (E=3e-12)
- (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_218408.1)
- Domains: Pfam-A via hmmscan --cut_ga — WXG100 (PF06013.19)
- 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
2A33T - Curated reference: UniProt O05453 (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 —
8 functional partner(s); context anchor
esxC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004125|Rv3891c|esxD MADTIQVTPQMLRSTANDIQANMEQAMGIAKGYLANQENVMNPATWSGAGVVASHMTATEITNELNKVLTGGTRLAEGLVQAAALMEGHEADSQTAFQALFGASHGS