Rv0890c Family assigned · medium auto-curated
H37Rv Rv0890c · MTBC0 - ·
882 aa · 989948–992596 (-) ·
RefSeq NP_215405.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | HTH-type transcriptional regulator. Pfam: HTH_77 (PF25872.1), GerE (PF00196.26), Sigma70_r4_2 (PF08281.19). |
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 |
P9WMG1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative HTH-type transcriptional regulator Rv0890c |
UniProt still lists this protein as Putative HTH-type transcriptional regulator Rv0890c; the revised annotation above is ahead of the current UniProt record.
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 | COG2197 |
| Gene Ontology (13) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0008150, GO:0030312, GO:0040007, GO:0044424, GO:0044444, GO:0044464 +1 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 | 0.461 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 13 synonymous, 16 missense, 1 nonsense, 5 frameshift |
| Disruption | 6 distinct premature-stop/frameshift site(s); most common in 0.59% of strains (850) · 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 | 1.4e-08 | 232–305 | Winged helix-turn-helix domain |
GerE | PF00196.26 | 1.3e-18 | 820–874 | Bacterial regulatory proteins, luxR family |
Sigma70_r4_2 | PF08281.19 | 1.3e-06 | 820–863 | Sigma-70, region 4 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: embR (transcriptional regulator EmbR), high confidence from genomic context alone (score 703 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0891c hyp |
hypothetical protein | 921 | 921 ctx | neighborhood:773 cooccurence:513 |
Rv1267c embR |
transcriptional regulator EmbR | 719 | 703 ctx | fusion:638 |
Rv1359 |
transcriptional regulator | 618 | 619 ctx | cooccurence:567 |
Rv0889c citA |
citrate synthase 2 | 583 | 584 ctx | neighborhood:567 |
Rv0845 narS |
sensor histidine kinase NarS | 592 | 573 | |
Rv3132c devS |
two component sensor histidine kinase DevS | 646 | 563 | |
Rv2027c dosT |
two component sensor histidine kinase DosT | 593 | 551 | |
Rv3124 moaR1 |
transcriptional regulator MoaR | 501 | 473 | |
Rv3899c hyp |
hypothetical protein | 437 | 417 | |
Rv3365c hyp |
hypothetical protein | 412 | 390 | |
Rv0977 PE_PGRS16 |
PE-PGRS family protein PE_PGRS16 | 400 | 378 | |
Rv1747 |
ABC transporter ATP-binding protein/permease | 436 | 247 | |
Rv0442c PPE10 |
PPE family protein PPE10 | 404 | 227 | |
Rv0928 pstS3 |
phosphate ABC transporter substrate-binding lipoprotein PstS | 428 | 193 | |
Rv1354c hyp |
hypothetical protein | 442 | 176 |
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): HTH-type transcriptional regulator
- Pfam (hmmscan --cut_ga): HTH_77 PF25872.1 (E=1e-08), GerE PF00196.26 (E=1e-18), Sigma70_r4_2 PF08281.19 (E=1e-06)
- (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_215405.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_77 (PF25872.1), GerE (PF00196.26), Sigma70_r4_2 (PF08281.19)
- 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
COG2197 - Curated reference: UniProt P9WMG1 (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 —
27 functional partner(s); context anchor
embR - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0890c| MRALLAQNRLVTLCGTGGVGKTRLAIQIASASELRDGLCFVDLAPITESGIVAATAARAVGLPDQPGRSTMDSLRRFIGNRRMLMVLDNCEHLLDACAALVVELLGACPELTILATSREPIGMAGEITWRVPSMSITDEAVELFADRASRVQPGFTIANHNAAAVGEICRRLDGIPLAIEFAAARVRSMSPLEIADGLDDCFRLLAGGVRGAVQRQQTLRASIDWSHALLTETEQILFRRLAPFVGGFDLAAVRAVAAGSDLDPFSVLDQLTLLVDKSLVVADDCQGRTRYRLLETVRRYALEKLGDSGEADVHARHRDYYTALAASLNTPADNDHQRLVARAETEIDNLRAAFAWSRENGHITEALQLASSLQPIWFGRAHLREGLSWFNSILEDQRFHRLAVSTAVRARALADKAMLSTWLATSPVGATDIIAPAQQALAMAREVGDPAALVRALTACGCSSGYNAEAAAPYFAEATDLARAIDDKWTLCQILYWRGVGTCISGDPNALRAAAEECRDLADTIGDRFVSRHCSLWLSLAQMWAGNLTEALELSREITAEAEASNDVPTKVLGLYTQAQVLAYCGASAAHAIAGACIAAATELGGVYQGIGYAAMTYAALAAGDVTAALEASDAARPILRAQPDQVTMHQVLMAQLALAGGDAIAARQFANDAVDATNGWHRMVALTIRARVATARGEPELARDDAHAALACGAELHIYQGMPDAMELLAGLAGEVGSHSEGVRLLGAAAALRQQTRQVRFKIWDAGYQASVTALREAMGDEDFDRAWAEGAALSTDEAIAYAQRGRGERKRPARGWGSLTPTERDVVRLVSEGLSNKDIAKRLFVSPRTVQTHLTHVYAKLGLPSRVQLVDEAARRGSPS