Rv1626 Family assigned · medium auto-curated
H37Rv Rv1626 · MTBC0 mtbc0_001734 ·
205 aa · 1840144–1840761 (+) ·
RefSeq NP_216142.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | two-component system transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | ANTAR domain-containing response regulator |
| Revised (this work) | ANTAR domain-containing response regulator. Pfam: Response_reg (PF00072.31), ANTAR (PF03861.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGM3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Transcriptional regulatory protein PdtaR |
| Curated function | Member of the two-component regulatory system PdtaR/PdtaS. This two-component system plays an essential role in mycobacterial adaptation to poor nutrient conditions. PdtaR probably acts at the level of transcriptional antitermination rather than transcriptional initiation..; FUNCTION: In addition, the PdtaR/PdtaS two-component system controls copper and nitric oxide (NO) resistance downstream of the intramembrane protease Rip1. This coupled Rip1/PdtaS/PdtaR circuit controls NO resistance and acute lung infection in mice by relieving PdtaR/PdtaS-mediated repression of isonitrile chalkophore bio. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| Preferred name | pdtaR |
| eggNOG description | response regulator |
| Orthologous group | COG3707 |
| KEGG orthology |
K22010
|
| KEGG modules |
M00839
|
| Gene Ontology (25) |
GO:0000160, GO:0003674, GO:0005488, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0007154, GO:0007165, GO:0008150, GO:0009987, GO:0016020 +13 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 | 0.33 · 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-29 | 16–125 | Response regulator receiver domain |
ANTAR | PF03861.20 | 4.0e-20 | 144–195 | ANTAR domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pdtaS (two component sensor kinase), high confidence from genomic context alone (score 786 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1630 rpsA |
30S ribosomal protein S1 | 821 | 795 | coexpression:767 |
Rv3220c pdtaS |
two component sensor kinase | 984 | 786 ctx | cooccurence:756 textmining:928 |
Rv2239c hyp |
hypothetical protein | 732 | 732 | coexpression:732 |
Rv1310 atpD |
ATP synthase subunit beta | 734 | 730 | coexpression:730 |
Rv1311 atpC |
ATP synthase subunit epsilon | 687 | 687 | coexpression:687 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 651 | 651 | coexpression:651 |
Rv3859c gltB |
glutamate synthase large subunit | 637 | 587 ctx | neighborhood:544 |
Rv0491 regX3 |
two component sensory transduction protein RegX | 594 | 515 ctx | cooccurence:489 |
Rv1625c cya |
adenylate cyclase | 508 | 508 ctx | neighborhood:503 |
Rv2920c amt |
ammonium transporter integral membrane protein | 528 | 461 | coexpression:417 |
Rv0831c hyp |
hypothetical protein | 457 | 458 | coexpression:458 |
Rv1611 trpC |
indole-3-glycerol phosphate synthase | 453 | 453 | |
Rv1624c |
membrane protein | 449 | 448 ctx | neighborhood:440 |
Rv0758 phoR |
two component system response sensor kinase PhoR | 480 | 404 ctx | cooccurence:400 |
Rv2847c cysG |
multifunctional uroporphyrin-III C-methyltransferase/precorrin-2 oxidase/ferrochelatase | 537 | 371 |
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 system transcriptional regulator
- MTBC0 PGAP product: ANTAR domain-containing response regulator
- Pfam (hmmscan --cut_ga): Response_reg PF00072.31 (E=2e-29), ANTAR PF03861.20 (E=4e-20)
- (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_216142.1)
- Domains: Pfam-A via hmmscan --cut_ga — Response_reg (PF00072.31), ANTAR (PF03861.20)
- 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
COG3707 - Curated reference: UniProt P9WGM3 (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 —
33 functional partner(s); context anchor
pdtaS - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001734|Rv1626| MTGPTTDADAAVPRRVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAELHKPDLVIMDVKMPRRDGIDAASEIASKRIAPIVVLTAFSQRDLVERARDAGAMAYLVKPFSISDLIPAIELAVSRFREITALEGEVATLSERLETRKLVERAKGLLQTKHGMTEPDAFKWIQRAAMDRRTTMKRVAEVVLETLGTPKDT