kdpE Resolved · high auto-curated
H37Rv Rv1027c · MTBC0 mtbc0_001104 ·
226 aa · 1155764–1156444 (-) ·
RefSeq NP_215543.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator KdpE |
|---|---|
| MTBC0 PGAP re-annotation | two-component system response regulator KdpE |
| Revised (this work) | Two-component system response regulator KdpE. Pfam: Response_reg (PF00072.31), Trans_reg_C (PF00486.35). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGN1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Transcriptional regulatory protein KdpE |
| Curated function | Member of the two-component regulatory system KdpD/KdpE involved in the regulation of the kdp operon. Upon phosphorylation by KdpD, functions as a transcription regulator by direct binding to promoter regions of target genes to positively regulate their expression. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | kdpE |
| eggNOG description | transcriptional |
| Orthologous group | COG0745 |
| KEGG orthology |
K02483, K07667
|
| KEGG pathways |
map02020, map02024
|
| KEGG modules |
M00454
|
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.35 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.17% of strains (252) · 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 |
|---|---|---|---|---|
Response_reg | PF00072.31 | 7.8e-28 | 4–112 | Response regulator receiver domain |
Trans_reg_C | PF00486.35 | 8.9e-23 | 148–224 | Transcriptional regulatory protein, C terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: kdpD (sensor protein KdpD), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1028c kdpD |
sensor protein KdpD | 999 | 999 ctx | neighborhood:881 cooccurence:689 experimental:635 database:900 textmining:907 |
Rv1033c trcR |
two component transcriptional regulator TrcR | 922 | 919 ctx | neighborhood:544 coexpression:800 |
Rv1032c trcS |
two component sensor histidine kinase TrcS | 925 | 913 ctx | neighborhood:544 cooccurence:591 |
Rv2488c |
LuxR family transcriptional regulator | 893 | 881 | coexpression:861 |
Rv1029 kdpA |
potassium-transporting ATPase subunit A | 927 | 876 ctx | neighborhood:747 textmining:437 |
Rv0600c |
two component sensor kinase HK1 | 892 | 871 ctx | cooccurence:707 |
Rv0902c prrB |
two component sensor histidine kinase PrrB | 936 | 861 ctx | cooccurence:677 textmining:559 |
Rv1267c embR |
transcriptional regulator EmbR | 864 | 859 | coexpression:859 |
Rv1151c cobB |
NAD-dependent protein deacylase | 858 | 853 | coexpression:853 |
Rv1030 kdpB |
potassium-transporting ATPase subunit B | 900 | 850 ctx | neighborhood:747 |
Rv0117 oxyS |
oxidative stress response regulatory protein OxyS | 855 | 847 | coexpression:827 |
Rv1031 kdpC |
potassium-transporting ATPase subunit C | 908 | 846 ctx | neighborhood:747 textmining:434 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 855 | 846 | coexpression:828 |
Rv1359 |
transcriptional regulator | 845 | 844 | coexpression:824 |
Rv0602c tcrA |
two component DNA binding transcriptional regulator TcrA | 843 | 840 | coexpression:806 |
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 KdpE
- MTBC0 PGAP product: two-component system response regulator KdpE
- Pfam (hmmscan --cut_ga): Response_reg PF00072.31 (E=8e-28), Trans_reg_C PF00486.35 (E=9e-23)
- (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_215543.1)
- Domains: Pfam-A via hmmscan --cut_ga — Response_reg (PF00072.31), Trans_reg_C (PF00486.35)
- 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
COG0745 - Curated reference: UniProt P9WGN1 (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 —
104 functional partner(s); context anchor
kdpD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001104|Rv1027c|kdpE MTLVLVIDDEPQILRALRINLTVRGYQVITASTGAGALRAAAEHPPDVVILDLGLPDMSGIDVLGGLRGWLTAPVIVLSARTDSSDKVQALDAGADDYVTKPFGMDEFLARLRAAVRRNTAAAELEQPVIETDSFTVDLAGKKVIKDGAEVHLTPTEWGMLEMLARNRGKLVGRGELLKEVWGPAYATETHYLRVYLAQLRRKLEDDPSHPKHLLTESGMGYRFEA