Rv2488c Family assigned · medium auto-curated
H37Rv Rv2488c · MTBC0 - ·
1137 aa · 2797467–2800880 (-) ·
RefSeq NP_217004.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | LuxR family transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | LuxR family transcriptional regulator. Pfam: HTH_77 (PF25872.1), GerE (PF00196.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O53213
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | involved in signal transduction (via phosphorylation) involved in transcriptional regulatory mechanism and in the regulation of secondary metabolites catalytic activity ATP a protein ADP a phosphoprotein |
| Orthologous group | COG2114 |
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 | 0.814 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 10 synonymous, 21 missense, 1 nonsense, 3 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 17.38% of strains (25238) · convergent |
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 |
|---|---|---|---|---|
HTH_77 | PF25872.1 | 4.8e-09 | 487–557 | Winged helix-turn-helix domain |
GerE | PF00196.26 | 1.3e-15 | 1070–1122 | Bacterial regulatory proteins, luxR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: embR (transcriptional regulator EmbR), high confidence from genomic context alone (score 931 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 935 | 932 | coexpression:856 experimental:440 |
Rv1267c embR |
transcriptional regulator EmbR | 935 | 931 ctx | fusion:454 coexpression:859 |
Rv1027c kdpE |
transcriptional regulator KdpE | 893 | 881 | coexpression:861 |
Rv1931c |
transcriptional regulator | 885 | 879 | coexpression:857 |
Rv1189 sigI |
ECF RNA polymerase sigma factor SigI | 868 | 860 | coexpression:829 |
Rv1359 |
transcriptional regulator | 846 | 847 | coexpression:805 |
Rv1725c hyp |
hypothetical protein | 851 | 846 | coexpression:846 |
Rv1190 hyp |
hypothetical protein | 847 | 846 | coexpression:845 |
Rv3840 |
transcriptional regulator | 845 | 843 | coexpression:843 |
Rv3736 |
AraC/XylS family transcriptional regulator | 850 | 842 | coexpression:841 |
Rv3164c moxR3 |
methanol dehydrogenase transcriptional regulator MoxR | 839 | 840 | coexpression:836 |
Rv3263 |
DNA methylase | 839 | 839 | coexpression:839 |
Rv3328c sigJ |
ECF RNA polymerase sigma factor SigJ | 846 | 837 | coexpression:804 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 844 | 837 | coexpression:836 |
Rv3167c |
TetR family transcriptional regulator | 844 | 836 | 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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): LuxR family transcriptional regulator
- Pfam (hmmscan --cut_ga): HTH_77 PF25872.1 (E=5e-09), GerE PF00196.26 (E=1e-15)
- (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_217004.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_77 (PF25872.1), 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
COG2114 - Curated reference: UniProt O53213 (TrEMBL, unreviewed; 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 —
120 functional partner(s); context anchor
embR - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2488c| MDRRPRDFEQSRRRCRCNALRAGSMLASMSKIHPGVDVVPVDWSADGVSELVPTGTVTLLLADIEGATHLPGSQLDTTAIAKLDRTLTELVREHRGVCPVEQGEGDSFLVAFARASDAVACALGLQRAPLAPIRLRIGMHTGEVSSPDEGNCVGPTIDRTARLRELAHGGQTVLSGTTSDLVADLLPKDAWLNDLGTYRLDDLPRPERVVQLCHPDLHNAFPPLRTRKVVGAHCLPAQLTRLVGRVDEVAQVRGLLDVKRWVTLTGVGGVGKTRLATQVASAVADGYPDGVWYVNLAPITDPALVPIAAARVLGLPDQPGRSTVDTIVRRIGDRRMLVVLDNCEHLLDGCAALIVALLGACPALRVLATSREPIAVAGEQIWRVPPLGHGEAIELFTDRAREARPELEITADNLALVTEICHRLDGIPLAIELAASRVRALALTEIVDSLHDRFRLLTGGSRIAVRRQQTMRASVDWSHALLTGPEQVLFRRLAVFPSGFDLDGAQAAAAGGDVQRYEVVDLLSLLADKSLVVTDDSDGRTRYRLLETVRQYALEKLRESGDADAVRARHRDHYAAVAAGLDAPSVAGHERRLNQAELEIDNLRAAFAFSRENGDTGHALLLASCLQPLWRARGRLQEGLAWFAAALADHDAHPAGADPGLYARALADRALIDAVAGITDRLDDAQKALAIARDIEDPALLARALTACGGVAAYNADLARPWLAEAVGLARAVGDKWRLAEVLAWQAYVGFAGEGDPGATRAAGEEARSLADEIGDAFLSRSCRWALAAANLWQGNLEAAVGLSREVIGESDAAHDMVSSCAGQACLAHALAHRGDTEAAAAAQASIDTAVGLSPVLSGSACSALVFATLAAGDVAAAEHARESATRFFGASAAAIINDPTSSAQISCARGDLNAAHRLADGAASITRGVHRARALTTRCRIEIAQGDRHRAERDAHDALGVAASIGAYLWVPDILECLASVMADAGSNREAVRLFGAADAARGRMGAVRFGIYQAGCNSSLATLRKSMGDSEFDDAWAEGTALSIDEAIAYAQRGRGARKRPTSGWGALTPTELEVALLVGEGLSNKEIGVRLFISPRTVHSHLTHVYTKLGLSSRLQLAQQAARRGESERGPSRP