espR Family assigned · low auto-curated
H37Rv Rv3849 · MTBC0 mtbc0_004082 ·
132 aa · 4347609–4348007 (+) ·
RefSeq NP_218366.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-1 transcriptional regulator EspR |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-1 transcriptional regulator EspR |
| Revised (this work) | Type VII secretion system ESX-1 transcriptional regulator EspR. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJB7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Nucleoid-associated protein EspR |
| Curated function | Virulence regulator that has both architectural and regulatory roles. Impacts cell wall functions and pathogenesis through regulation of multiple genes, including the espACD operon, which is a key ESX-1 component. Influences target gene expression positively or negatively, depending on its binding position relative to the genes it controls. Acts by binding directly to the DNA. May play a central role in regulating virulence gene expression. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | espR |
| eggNOG description | transcriptional regulators |
| Orthologous group | COG1476 |
| Gene Ontology (68) |
GO:0002791, GO:0003674, GO:0003676, GO:0003677, GO:0005488, GO:0005515, GO:0005575, GO:0005576, GO:0005618, GO:0005622, GO:0005623, GO:0005737 +56 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 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: Rv0882 (transmembrane protein), medium confidence from genomic context alone (score 682 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3850 hyp |
hypothetical protein | 854 | 813 ctx | neighborhood:712 |
Rv0882 |
transmembrane protein | 681 | 682 ctx | cooccurence:680 |
Rv3647c hyp |
hypothetical protein | 673 | 673 ctx | cooccurence:668 |
Rv1109c hyp |
hypothetical protein | 662 | 663 ctx | cooccurence:652 |
Rv2091c |
membrane protein | 613 | 613 ctx | cooccurence:593 |
Rv1222 rseA |
anti-sigma E factor RseA | 623 | 608 ctx | cooccurence:598 |
Rv1166 lpqW |
monoacyl phosphatidylinositol tetramannoside-binding protein LpqW | 615 | 601 ctx | cooccurence:598 |
Rv0481c hyp |
hypothetical protein | 596 | 597 ctx | cooccurence:593 |
Rv3822 chp1 hyp |
hypothetical protein | 580 | 580 | coexpression:580 |
Rv3527 hyp |
hypothetical protein | 575 | 575 ctx | cooccurence:574 |
Rv2049c hyp |
hypothetical protein | 549 | 549 ctx | cooccurence:548 |
Rv0996 |
transmembrane protein | 617 | 536 ctx | cooccurence:535 |
Rv3851 |
membrane protein | 531 | 531 ctx | neighborhood:526 |
Rv3004 cfp6 |
low molecular weight protein antigen 6 | 524 | 524 ctx | cooccurence:524 |
Rv2042c hyp |
hypothetical protein | 519 | 519 ctx | cooccurence:519 |
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 transcriptional regulator EspR
- MTBC0 PGAP product: type VII secretion system ESX-1 transcriptional regulator EspR
- (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_218366.1)
- 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
COG1476 - Curated reference: UniProt P9WJB7 (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 —
69 functional partner(s); context anchor
Rv0882 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004082|Rv3849|espR MSTTFAARLNRLFDTVYPPGRGPHTSAEVIAALKAEGITMSAPYLSQLRSGNRTNPSGATMAALANFFRIKAAYFTDDEYYEKLDKELQWLCTMRDDGVRRIAQRAHGLPSAAQQKVLDRIDELRRAEGIDA