trcR Resolved · high auto-curated
H37Rv Rv1033c · MTBC0 mtbc0_001112 ·
257 aa · 1165300–1166073 (-) ·
RefSeq NP_215549.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | two component transcriptional regulator TrcR |
|---|---|
| MTBC0 PGAP re-annotation | two-component system response regulator TrcR |
| Revised (this work) | Two-component system response regulator TrcR. 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 |
L7N689
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Transcriptional regulatory protein TrcR |
| Curated function | Member of the two-component regulatory system TrcS/TrcR. Activates its own expression by binding specifically to the AT-rich sequence of the trcR promoter region. Also negatively regulates the expression of Rv1057 by binding to an AT-rich sequences within the Rv1057 upstream sequence. The TrcR-TrcS regulatory system may act as a transition regulatory system involved in adapting to an intracellular environment and transitioning from latency to reactivation. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K TranscriptionT Signal transduction mechanisms
|
|---|---|
| Preferred name | trcR |
| eggNOG description | transcriptional |
| Orthologous group | COG0745 |
| KEGG orthology |
K02483, K07672
|
| KEGG pathways |
map02020
|
| KEGG modules |
M00463
|
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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Response_reg | PF00072.31 | 2.9e-28 | 34–143 | Response regulator receiver domain |
Trans_reg_C | PF00486.35 | 1.1e-26 | 179–253 | Transcriptional regulatory protein, C terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: trcS (two component sensor histidine kinase TrcS), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1032c trcS |
two component sensor histidine kinase TrcS | 999 | 999 ctx | neighborhood:881 cooccurence:769 database:900 textmining:830 |
Rv1027c kdpE |
transcriptional regulator KdpE | 922 | 919 ctx | neighborhood:544 coexpression:800 |
Rv3764c tcrY |
two component sensor kinase TcrY | 915 | 899 ctx | cooccurence:766 |
Rv0600c |
two component sensor kinase HK1 | 913 | 891 ctx | cooccurence:755 |
Rv0902c prrB |
two component sensor histidine kinase PrrB | 948 | 888 ctx | cooccurence:736 textmining:561 |
Rv0982 mprB |
two component histidine-protein kinase/phosphatase MprB | 870 | 866 ctx | cooccurence:691 |
Rv0490 senX3 |
two component sensor histidine kinase SenX3 | 887 | 855 ctx | cooccurence:744 |
Rv0758 phoR |
two component system response sensor kinase PhoR | 896 | 853 ctx | cooccurence:743 |
Rv0273c |
transcriptional regulator | 831 | 831 | coexpression:831 |
Rv2488c |
LuxR family transcriptional regulator | 845 | 828 | coexpression:799 |
Rv3164c moxR3 |
methanol dehydrogenase transcriptional regulator MoxR | 760 | 759 | coexpression:759 |
Rv3245c mtrB |
two component sensory histidine kinase MtrB | 800 | 746 ctx | cooccurence:558 |
Rv1151c cobB |
NAD-dependent protein deacylase | 744 | 735 | coexpression:734 |
Rv1681 moeX |
molybdopterin biosynthesis protein MoeX | 735 | 734 | coexpression:734 |
Rv3488 hyp |
hypothetical protein | 734 | 734 | coexpression:734 |
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 TrcR
- MTBC0 PGAP product: two-component system response regulator TrcR
- Pfam (hmmscan --cut_ga): Response_reg PF00072.31 (E=3e-28), Trans_reg_C PF00486.35 (E=1e-26)
- (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_215549.1)
- 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 L7N689 (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 —
52 functional partner(s); context anchor
trcS - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001112|Rv1033c|trcR MTTMSGYTRSQRPRQAILGQLPRIHRADGSPIRVLLVDDEPALTNLVKMALHYEGWDVEVAHDGQEAIAKFDKVGPDVLVLDIMLPDVDGLEILRRVRESDVYTPTLFLTARDSVMDRVTGLTSGADDYMTKPFSLEELVARLRGLLRRSSHLERPADEALRVGDLTLDGASREVTRDGTPISLSSTEFELLRFLMRNPRRALSRTEILDRVWNYDFAGRTSIVDLYISYLRKKIDSDREPMIHTVRGIGYMLRPPE