Rv1828 Family assigned · medium auto-curated
H37Rv Rv1828 · MTBC0 mtbc0_001942 ·
247 aa · 2091169–2091912 (+) ·
RefSeq NP_216344.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | MerR family transcriptional regulator |
| Revised (this work) | MerR family transcriptional regulator. Pfam: MerR (PF00376.30), MerR_1 (PF13411.13), HTH_Rv1828 (PF28507.1). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WME7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized HTH-type transcriptional regulator Rv1828 |
| Curated function | Transcriptional regulator that binds to its own promoter and thus may play a role in the regulation of the cotranscribed genes Rv1827 and Rv1828. Can also bind several promoter regions of genes that are essential, including ftsZ. Binds to the imperfect everted repeat sequence CTCAA through its winged-HTH motif. |
UniProt still lists this protein as Uncharacterized HTH-type transcriptional regulator Rv1828; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | merR1 |
| eggNOG description | Transcriptional regulator |
| Orthologous group | COG0789 |
| Gene Ontology (10) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0008150, GO:0040007, GO:0044424, GO:0044444, GO:0044464
|
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 | 0.258 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 2 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 |
|---|---|---|---|---|
MerR | PF00376.30 | 1.3e-06 | 27–54 | MerR family regulatory protein |
MerR_1 | PF13411.13 | 1.2e-07 | 28–84 | MerR HTH family regulatory protein |
HTH_Rv1828 | PF28507.1 | 9.5e-40 | 127–244 | Rv1828-like, helix-turn-helix domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: garA (glycogen accumulation regulator GarA), high confidence from genomic context alone (score 912 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1827 garA |
glycogen accumulation regulator GarA | 918 | 912 ctx | neighborhood:882 |
Rv1332 |
transcriptional regulator | 779 | 771 | coexpression:771 |
Rv1829 hyp |
hypothetical protein | 829 | 769 ctx | neighborhood:763 |
Rv1826 gcvH |
glycine cleavage system protein H | 709 | 710 ctx | neighborhood:706 |
Rv1824 hyp |
hypothetical protein | 696 | 696 ctx | neighborhood:692 |
Rv1823 hyp |
hypothetical protein | 684 | 684 ctx | neighborhood:676 |
Rv1822 pgsA2 |
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | 667 | 667 ctx | neighborhood:665 |
Rv1830 |
HTH-type transcriptional regulator | 716 | 613 ctx | neighborhood:463 |
Rv1821 secA2 |
accessory Sec system translocase SecA2 | 616 | 597 ctx | neighborhood:584 |
Rv0352 dnaJ1 |
chaperone protein DnaJ | 611 | 586 | experimental:469 |
Rv2373c dnaJ2 |
chaperone protein DnaJ | 609 | 585 | experimental:469 |
Rv2860c glnA4 |
glutamine synthetase | 595 | 574 | |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 582 | 566 | experimental:463 |
Rv1825 hyp |
hypothetical protein | 556 | 556 ctx | neighborhood:536 |
Rv2220 glnA1 |
glutamine synthetase | 547 | 524 |
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: HTH-type transcriptional regulator
- MTBC0 PGAP product: MerR family transcriptional regulator
- Pfam (hmmscan --cut_ga): MerR PF00376.30 (E=1e-06), MerR_1 PF13411.13 (E=1e-07), HTH_Rv1828 PF28507.1 (E=1e-39)
- (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_216344.1)
- Domains: Pfam-A via hmmscan --cut_ga — MerR (PF00376.30), MerR_1 (PF13411.13), HTH_Rv1828 (PF28507.1)
- 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
COG0789 - Curated reference: UniProt P9WME7 (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 —
37 functional partner(s); context anchor
garA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001942|Rv1828| MSAPDSPALAGMSIGAVLDLLRPDFPDVTISKIRFLEAEGLVTPRRASSGYRRFTAYDCARLRFILTAQRDHYLPLKVIRAQLDAQPDGELPPFGSPYVLPRLVPVAGDSAGGVGSDTASVSLTGIRLSREDLLERSEVADELLTALLKAGVITTGPGGFFDEHAVVILQCARALAEYGVEPRHLRAFRSAADRQSDLIAQIAGPLVKAGKAGARDRADDLAREVAALAITLHTSLIKSAVRDVLHR