Rv0023 Family assigned · medium auto-curated
H37Rv Rv0023 · MTBC0 mtbc0_000028 ·
256 aa · 27577–28347 (+) ·
RefSeq NP_214537.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | helix-turn-helix transcriptional regulator |
| Revised (this work) | Helix-turn-helix transcriptional regulator. Pfam: HTH_31 (PF13560.13), HTH_3 (PF01381.29). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMI3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized HTH-type transcriptional regulator Rv0023 |
UniProt still lists this protein as Uncharacterized HTH-type transcriptional regulator Rv0023; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Helix-turn-helix |
| Orthologous group | COG1396 |
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 | 0.36 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 7 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_31 | PF13560.13 | 7.8e-09 | 7–61 | Helix-turn-helix domain |
HTH_3 | PF01381.29 | 6.2e-11 | 10–61 | Helix-turn-helix |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0024 (NLP/P60 family protein), high confidence from genomic context alone (score 826 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0025 hyp |
hypothetical protein | 833 | 833 ctx | neighborhood:826 |
Rv0024 |
NLP/P60 family protein | 825 | 826 ctx | neighborhood:816 |
Rv0022c whiB5 |
transcriptional regulator WhiB5 | 773 | 773 ctx | neighborhood:771 |
Rv0028 hyp |
hypothetical protein | 670 | 670 ctx | neighborhood:670 |
Rv0027 hyp |
hypothetical protein | 670 | 670 ctx | neighborhood:670 |
Rv0026 hyp |
hypothetical protein | 511 | 512 ctx | neighborhood:507 |
Rv0332 hyp |
hypothetical protein | 500 | 473 | experimental:434 |
Rv0366c hyp |
hypothetical protein | 476 | 448 | experimental:434 |
Rv3202c adnA |
ATP-dependent DNA helicase | 531 | 70 | textmining:517 |
Rv0081 |
HTH-type transcriptional regulator | 541 | 63 | textmining:531 |
Rv1657 argR |
arginine repressor | 547 | 61 | textmining:538 |
Rv2034 |
ArsR family HTH-type transcriptional repressor | 502 | 58 | textmining:493 |
Rv2506 |
TetR family transcriptional regulator | 554 | 55 | textmining:548 |
Rv3164c moxR3 |
methanol dehydrogenase transcriptional regulator MoxR | 443 | 52 | textmining:437 |
Rv1423 whiA |
transcriptional regulator WhiA | 679 | 49 | textmining:676 |
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: helix-turn-helix transcriptional regulator
- Pfam (hmmscan --cut_ga): HTH_31 PF13560.13 (E=8e-09), HTH_3 PF01381.29 (E=6e-11)
- (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_214537.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_31 (PF13560.13), HTH_3 (PF01381.29)
- 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
COG1396 - Curated reference: UniProt P9WMI3 (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 —
22 functional partner(s); context anchor
Rv0024 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000028|Rv0023| MSRESAGAAIRALRESRDWSLADLAAATGVSTMGLSYLERGARKPHKSTVQKVENGLGLPPGTYSRLLVAADPDAELARLIAAQPSNPTAVRRAGAVVVDRHSDTDVLEGYAEAQLDAIKSVIDRLPATTSNEYETYILSVIAQCVKAEMLAASSWRVAVNAGADSTGRLMEHLRALEATRGALLERMPTSLSARFDRACAQSSLPEAVVAALIGVGADEMWDIRNRGVIPAGALPRVRAFVDAIEASHDADEGQQ