Rv1830 Family assigned · medium auto-curated
H37Rv Rv1830 · MTBC0 - ·
225 aa · 2074841–2075518 (+) ·
RefSeq NP_216346.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | HTH-type transcriptional regulator. Pfam: MerR_1 (PF13411.13). |
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 |
P9WME5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized HTH-type transcriptional regulator Rv1830 |
UniProt still lists this protein as Uncharacterized HTH-type transcriptional regulator Rv1830; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | merR2 |
| eggNOG description | transcriptional |
| Orthologous group | COG0789 |
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 | 0.344 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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_1 | PF13411.13 | 1.9e-12 | 69–135 | MerR HTH family regulatory protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpoZ (DNA-directed RNA polymerase subunit omega), high confidence from genomic context alone (score 870 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 875 | 870 ctx | cooccurence:757 experimental:463 |
Rv1440 secG |
protein-export membrane protein SecG | 796 | 796 ctx | cooccurence:771 |
Rv3260c whiB2 |
transcriptional regulator WhiB2 | 843 | 779 ctx | cooccurence:770 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 776 | 776 ctx | cooccurence:766 |
Rv3219 whiB1 |
transcriptional regulator WhiB1 | 775 | 775 ctx | cooccurence:772 |
Rv2699c hyp |
hypothetical protein | 772 | 772 ctx | cooccurence:771 |
Rv2219 |
transmembrane protein | 750 | 751 ctx | cooccurence:747 |
Rv1321 nucS |
endonuclease NucS | 734 | 735 ctx | cooccurence:731 |
Rv2901c hyp |
hypothetical protein | 732 | 733 ctx | cooccurence:730 |
Rv1423 whiA |
transcriptional regulator WhiA | 754 | 719 ctx | cooccurence:716 |
Rv3195 hyp |
hypothetical protein | 717 | 718 ctx | cooccurence:717 |
Rv3681c whiB4 |
transcriptional regulator WhiB4 | 719 | 708 ctx | cooccurence:705 |
Rv2256c hyp |
hypothetical protein | 693 | 694 ctx | cooccurence:689 |
Rv2696c hyp |
hypothetical protein | 689 | 690 ctx | cooccurence:688 |
Rv2413c hyp |
hypothetical protein | 684 | 685 ctx | cooccurence:675 |
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): MerR_1 PF13411.13 (E=2e-12)
- (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_216346.1)
- Domains: Pfam-A via hmmscan --cut_ga — MerR_1 (PF13411.13)
- 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 P9WME5 (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 —
74 functional partner(s); context anchor
rpoZ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1830| MTQLVTRARSARGSTLGEQPRQDQLDFADHTGTAGDGNDGAAAASGPVQPGLFPDDSVPDELVGYRGPSACQIAGITYRQLDYWARTSLVVPSIRSAAGSGSQRLYSFKDILVLKIVKRLLDTGISLHNIRVAVDHLRQRGVQDLANITLFSDGTTVYECTSAEEVVDLLQGGQGVFGIAVSGAMRELTGVIADFHGERADGGESIAAPEDELASRRKHRDRKIG