Rv0081 Family assigned · medium auto-curated
H37Rv Rv0081 · MTBC0 mtbc0_000091 ·
114 aa · 89738–90082 (+) ·
RefSeq NP_214595.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | lsr2/espR transcriptional regulator |
| Revised (this work) | Lsr2/espR transcriptional regulator. Pfam: HTH_20 (PF12840.14), HTH_5 (PF01022.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMI7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized HTH-type transcriptional regulator Rv0081 |
UniProt still lists this protein as Uncharacterized HTH-type transcriptional regulator Rv0081; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | transcriptional |
| Orthologous group | COG0640 |
| KEGG orthology |
K03892
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.195 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 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_20 | PF12840.14 | 3.2e-06 | 17–64 | Helix-turn-helix domain |
HTH_5 | PF01022.27 | 1.1e-07 | 19–64 | Bacterial regulatory protein, arsR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0082 (oxidoreductase), high confidence from genomic context alone (score 975 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0082 |
oxidoreductase | 985 | 975 ctx | neighborhood:881 coexpression:800 textmining:433 |
Rv0083 |
oxidoreductase | 979 | 974 ctx | neighborhood:881 coexpression:751 |
Rv0085 hycP |
hydrogenase HycP | 944 | 921 ctx | neighborhood:874 |
Rv0086 hycQ |
hydrogenase HycQ | 928 | 907 ctx | neighborhood:874 |
Rv0084 hycD |
formate hydrogenlyase HycD | 906 | 902 ctx | neighborhood:881 |
Rv0087 hycE |
formate hydrogenase HycE | 948 | 897 ctx | neighborhood:874 textmining:516 |
Rv0080 hyp |
hypothetical protein | 877 | 687 ctx | neighborhood:579 textmining:625 |
Rv0088 |
polyketide cyclase/dehydrase | 751 | 667 ctx | neighborhood:651 |
Rv0079 hyp |
hypothetical protein | 787 | 583 ctx | neighborhood:579 textmining:511 |
Rv0827c kmtR |
HTH-type transcriptional regulator KmtR | 556 | 443 ctx | cooccurence:441 |
Rv2358 smtB |
HTH-type transcriptional regulator SmtB | 664 | 432 ctx | cooccurence:432 textmining:433 |
Rv0089 |
methyltransferase | 423 | 419 ctx | neighborhood:414 |
Rv3744 nmtR |
HTH-type transcriptional regulator NmtR | 465 | 388 | |
Rv3131 |
NAD(P)H nitroreductase | 526 | 193 | textmining:438 |
Rv3133c devR |
two component transcriptional regulator DevR | 878 | 70 | textmining:875 |
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: HTH-type transcriptional regulator
- MTBC0 PGAP product: lsr2/espR transcriptional regulator
- Pfam (hmmscan --cut_ga): HTH_20 PF12840.14 (E=3e-06), HTH_5 PF01022.27 (E=1e-07)
- (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_214595.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_20 (PF12840.14), HTH_5 (PF01022.27)
- 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
COG0640 - Curated reference: UniProt P9WMI7 (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 —
23 functional partner(s); context anchor
Rv0082 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000091|Rv0081| MESEPLYKLKAEFFKTLAHPARIRILELLVERDRSVGELLSSDVGLESSNLSQQLGVLRRAGVVAARRDGNAMIYSIAAPDIAELLAVARKVLARVLSDRVAVLEDLRAGGSAT