embR Resolved · high auto-curated
H37Rv Rv1267c · MTBC0 mtbc0_001357 ·
388 aa · 1425164–1426330 (-) ·
RefSeq NP_215783.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator EmbR |
|---|---|
| MTBC0 PGAP re-annotation | response regulator transcription factor EmbR |
| Revised (this work) | Response regulator transcription factor EmbR. Pfam: Trans_reg_C (PF00486.35), BTAD (PF03704.24), Yop-YscD_cpl (PF16697.11), FHA (PF00498.32). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGJ9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Transcriptional regulatory protein EmbR |
| Curated function | Positively regulates the transcription of the embCAB operon. Exhibits ATPase and GTPase activities. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | embR |
| eggNOG description | involved in transcriptional mechanism. thought to regulate the biosynthesis of the mycobacterial cell wall arabinan and resistance to ethambutol (Emb |
| Orthologous group | COG1716 |
| Gene Ontology (41) |
GO:0003674, GO:0003676, GO:0003677, GO:0003824, GO:0003924, GO:0005488, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006355, GO:0008150 +29 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 | 0.582 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 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 |
|---|---|---|---|---|
Trans_reg_C | PF00486.35 | 1.8e-10 | 31–103 | Transcriptional regulatory protein, C terminal |
BTAD | PF03704.24 | 2.2e-49 | 110–255 | Bacterial transcriptional activator domain |
Yop-YscD_cpl | PF16697.11 | 1.4e-10 | 297–378 | Inner membrane component of T3SS, cytoplasmic domain |
FHA | PF00498.32 | 1.0e-17 | 308–371 | FHA domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0894 (transcriptional regulator), high confidence from genomic context alone (score 967 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0894 |
transcriptional regulator | 968 | 967 ctx | fusion:774 coexpression:800 |
Rv2488c |
LuxR family transcriptional regulator | 935 | 931 ctx | fusion:454 coexpression:859 |
Rv0339c iniR |
transcriptional regulator | 899 | 897 ctx | cooccurence:506 coexpression:800 |
Rv3263 |
DNA methylase | 875 | 876 | coexpression:850 |
Rv1963c mce3R |
transcriptional repressor Mce3R | 870 | 868 | coexpression:815 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 863 | 860 | coexpression:860 |
Rv3167c |
TetR family transcriptional regulator | 863 | 860 | coexpression:860 |
Rv1931c |
transcriptional regulator | 862 | 860 | coexpression:860 |
Rv1151c cobB |
NAD-dependent protein deacylase | 860 | 860 | coexpression:860 |
Rv0212c nadR |
transcriptional regulator NadR | 860 | 860 | coexpression:860 |
Rv1674c |
transcriptional regulator | 860 | 860 | coexpression:860 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 860 | 860 | coexpression:860 |
Rv1027c kdpE |
transcriptional regulator KdpE | 864 | 859 | coexpression:859 |
Rv3736 |
AraC/XylS family transcriptional regulator | 859 | 859 | coexpression:859 |
Rv3055 |
TetR family transcriptional regulator | 860 | 857 | coexpression:804 |
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: transcriptional regulator EmbR
- MTBC0 PGAP product: response regulator transcription factor EmbR
- Pfam (hmmscan --cut_ga): Trans_reg_C PF00486.35 (E=2e-10), BTAD PF03704.24 (E=2e-49), Yop-YscD_cpl PF16697.11 (E=1e-10), FHA PF00498.32 (E=1e-17)
- (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_215783.1)
- Domains: Pfam-A via hmmscan --cut_ga — Trans_reg_C (PF00486.35), BTAD (PF03704.24), Yop-YscD_cpl (PF16697.11), FHA (PF00498.32)
- 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
COG1716 - Curated reference: UniProt P9WGJ9 (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 —
122 functional partner(s); context anchor
Rv0894 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001357|Rv1267c|embR MAGSATVEKRLDFGLLGPLQMTIDGTPVPSGTPKQRAVLAMLVINRNRPVGVDALITALWEEWPPSGARASIHSYVSNLRKLLGGAGIDPRVVLAAAPPGYRLSIPDNTCDLGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRALNERILRQQPLDAKKSAKTTAAGTVTVLDQRTMASGQQAVAYLHDIASGRGYPLQAAATRIGRLHDNDIVLDSANVSRHHAVIVDTGTNYVINDLRSSNGVHVQHERIRSAVTLNDGDHIRICDHEFTFQISAGTHGGT