Rv0324 Family assigned · medium auto-curated
H37Rv Rv0324 · MTBC0 mtbc0_000345 ·
226 aa · 394675–395355 (+) ·
RefSeq NP_214838.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | metalloregulator ArsR/SmtB family transcription factor |
| Revised (this work) | Metalloregulator ArsR/SmtB family transcription factor. Pfam: HTH_5 (PF01022.27), HTH_IclR (PF09339.17), Rhodanese (PF00581.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O08446
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH-type transcriptional regulator Rv0324 |
| Curated function | Part of a regulatory network that coordinates tolerance to the antitubercular drug bedaquiline. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Rhodanese-like domain |
| Orthologous group | COG0607 |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 4 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 |
|---|---|---|---|---|
HTH_5 | PF01022.27 | 2.3e-06 | 26–69 | Bacterial regulatory protein, arsR family |
HTH_IclR | PF09339.17 | 1.9e-05 | 27–70 | IclR helix-turn-helix domain |
Rhodanese | PF00581.26 | 5.6e-20 | 121–210 | Rhodanese-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: arsC (arsenic-transport integral membrane protein ArsC), high confidence from genomic context alone (score 729 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0326 hyp |
hypothetical protein | 823 | 816 ctx | neighborhood:775 |
Rv0325 hyp |
hypothetical protein | 799 | 791 ctx | neighborhood:786 |
Rv2643 arsC |
arsenic-transport integral membrane protein ArsC | 805 | 729 ctx | neighborhood:479 |
Rv3846 sodA |
superoxide dismutase | 660 | 622 | experimental:573 |
Rv0323c hyp |
hypothetical protein | 601 | 601 ctx | neighborhood:596 |
Rv2367c ybeY |
endoribonuclease | 585 | 586 | experimental:573 |
Rv3456c rplQ |
50S ribosomal protein L17 | 531 | 531 | experimental:466 |
Rv3443c rplM |
50S ribosomal protein L13 | 515 | 516 | experimental:453 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 506 | 506 | experimental:476 |
Rv2442c rplU |
50S ribosomal protein L21 | 499 | 499 | experimental:466 |
Rv0640 rplK |
50S ribosomal protein L11 | 491 | 492 | experimental:461 |
Rv0715 rplX |
50S ribosomal protein L24 | 506 | 491 | experimental:453 |
Rv0701 rplC |
50S ribosomal protein L3 | 490 | 490 | experimental:450 |
Rv0723 rplO |
50S ribosomal protein L15 | 480 | 481 | experimental:453 |
Rv2234 ptpA |
protein-tyrosine-phosphatase | 495 | 448 |
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: transcriptional regulator
- MTBC0 PGAP product: metalloregulator ArsR/SmtB family transcription factor
- Pfam (hmmscan --cut_ga): HTH_5 PF01022.27 (E=2e-06), HTH_IclR PF09339.17 (E=2e-05), Rhodanese PF00581.26 (E=6e-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_214838.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_5 (PF01022.27), HTH_IclR (PF09339.17), Rhodanese (PF00581.26)
- 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
COG0607 - Curated reference: UniProt O08446 (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 —
40 functional partner(s); context anchor
arsC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000345|Rv0324| MAGQSDRKAALLDQVARVGKALANGRRLQILDLLAQGERAVEAIATATGMNLTTASANLQALKSGGLVEARREGTRQYYRIAGEDVARLFALVQVVADEHLADVAVAAADVLGSPEDAITRAELLRRREAGEVTLVDVRPHEEYQAGHIPGAINIPIAELADRLAELAGDRDIVAYCRGAYCVMAPDAVRIARDAGREVKRLDDGMLEWRLAGLPVDEGAPVGHGD