devR Resolved · high auto-curated
H37Rv Rv3133c · MTBC0 mtbc0_003330 ·
217 aa · 3520627–3521280 (-) ·
RefSeq NP_217649.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | two component transcriptional regulator DevR |
|---|---|
| MTBC0 PGAP re-annotation | two-component system response regulator DevR |
| Revised (this work) | Two-component system response regulator DevR. Pfam: Response_reg (PF00072.31), GerE (PF00196.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMF9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DNA-binding transcriptional activator DevR/DosR |
| Curated function | Member of the two-component regulatory system DevR/DevS (also called DosR/DosS) involved in onset of the dormancy response. Regulates an approximately 48-member regulon. When phosphorylated binds and activates the promoter of DevR regulon genes in response to hypoxia. The presence of target DNA increases stability of phospho-DevR in vitro. Activates its own transcription under hypoxic but not aerobic conditions, probably binds as a dimer to tandem binding sites within the devR and hspX promoters. Accepts a phosphate group from DevS (DosS) and from DosT. Does not regulate transcription of dosT. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | devR |
| eggNOG description | Regulator |
| Orthologous group | COG2197 |
| KEGG orthology |
K07695
|
| KEGG pathways |
map02020
|
| KEGG modules |
M00482
|
| Gene Ontology (90) |
GO:0001666, GO:0003674, GO:0003676, GO:0003677, GO:0003700, GO:0005488, GO:0005575, GO:0005576, GO:0005615, GO:0005618, GO:0005622, GO:0005623 +78 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 | 0.362 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Response_reg | PF00072.31 | 1.9e-23 | 4–115 | Response regulator receiver domain |
GerE | PF00196.26 | 5.8e-18 | 149–204 | Bacterial regulatory proteins, luxR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: devS (two component sensor histidine kinase DevS), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3132c devS |
two component sensor histidine kinase DevS | 999 | 1000 ctx | neighborhood:882 cooccurence:769 coexpression:895 experimental:544 database:900 textmining:963 |
Rv3134c |
universal stress protein | 991 | 954 ctx | neighborhood:744 coexpression:805 textmining:818 |
Rv2027c dosT |
two component sensor histidine kinase DosT | 993 | 883 ctx | cooccurence:767 textmining:946 |
Rv0845 narS |
sensor histidine kinase NarS | 884 | 853 ctx | cooccurence:726 |
Rv2005c |
universal stress protein | 866 | 849 | coexpression:848 |
Rv0569 hyp |
hypothetical protein | 900 | 832 | coexpression:810 textmining:433 |
Rv1736c narX |
nitrate reductase-like protein NarX | 905 | 805 | coexpression:799 textmining:535 |
Rv2029c pfkB |
6-phosphofructokinase PfkB | 901 | 805 | coexpression:734 textmining:515 |
Rv2623 TB31.7 |
universal stress protein | 932 | 802 | coexpression:772 textmining:671 |
Rv1997 ctpF |
cation transporter ATPase F | 869 | 779 | coexpression:762 textmining:435 |
Rv2625c rip3 |
zinc metalloprotease Rip3 | 880 | 765 | coexpression:765 textmining:512 |
Rv2028c |
universal stress protein | 910 | 752 | coexpression:703 textmining:652 |
Rv2004c hyp |
hypothetical protein | 834 | 733 | coexpression:732 textmining:404 |
Rv2629 hyp |
hypothetical protein | 794 | 732 | coexpression:732 |
Rv0195 |
two component transcriptional regulator | 780 | 704 ctx | cooccurence:703 |
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: two component transcriptional regulator DevR
- MTBC0 PGAP product: two-component system response regulator DevR
- Pfam (hmmscan --cut_ga): Response_reg PF00072.31 (E=2e-23), GerE PF00196.26 (E=6e-18)
- (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_217649.1)
- Domains: Pfam-A via hmmscan --cut_ga — Response_reg (PF00072.31), GerE (PF00196.26)
- 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
COG2197 - Curated reference: UniProt P9WMF9 (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 —
77 functional partner(s); context anchor
devS - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003330|Rv3133c|devR MVKVFLVDDHEVVRRGLVDLLGADPELDVVGEAGSVAEAMARVPAARPDVAVLDVRLPDGNGIELCRDLLSRMPDLRCLILTSYTSDEAMLDAILAGASGYVVKDIKGMELARAVKDVGAGRSLLDNRAAAALMAKLRGAAEKQDPLSGLTDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQAAVFATELKRSRPPGDGP