Rv0047c Family assigned · medium
H37Rv Rv0047c · MTBC0 mtbc0_000052 ·
180 aa · 51284–51826 (-) ·
RefSeq NP_214561.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | PadR family transcriptional regulator |
| Revised (this work) | PadR-family transcriptional regulator (Pfam PadR, PF03551). PadR repressors typically control detoxification and multidrug/stress-response genes; the regulon governed by this locus in M. tuberculosis is not established. |
Curated reference (UniProt)
| UniProt |
P71704
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Transcriptional regulator |
| Orthologous group | COG1695 |
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 | 0.701 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
PadR | PF03551.21 | 3.5e-21 | 6–81 | Transcriptional regulator PadR-like family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ino1 (inositol-3-phosphate synthase), high confidence from genomic context alone (score 841 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0046c ino1 |
inositol-3-phosphate synthase | 959 | 841 ctx | neighborhood:802 textmining:755 |
Rv0044c |
oxidoreductase | 726 | 727 ctx | neighborhood:725 |
Rv0045c |
hydrolase | 680 | 680 ctx | neighborhood:675 |
Rv0043c |
HTH-type transcriptional regulator | 633 | 630 ctx | neighborhood:625 |
Rv0048c |
membrane protein | 602 | 602 ctx | neighborhood:602 |
Rv0049 hyp |
hypothetical protein | 500 | 500 ctx | neighborhood:499 |
Rv2936 drrA |
daunorubicin ABC transporter ATP-binding protein DrrA | 445 | 445 | |
Rv1218c |
tetronasin ABC transporter ATP-binding protein | 440 | 440 | |
Rv2937 drrB |
daunorubicin ABC transporter permease DrrB | 436 | 437 ctx | cooccurence:411 |
Rv3364c hyp |
hypothetical protein | 422 | 422 ctx | cooccurence:421 |
Rv1687c |
ABC transporter ATP-binding protein | 419 | 420 | |
Rv1747 |
ABC transporter ATP-binding protein/permease | 574 | 374 | |
Rv0037c |
MFS-type transporter | 566 | 279 | textmining:424 |
Rv1683 |
bifunctional long-chain acyl-CoA synthase/lipase | 676 | 78 | textmining:664 |
Rv2011c hyp |
hypothetical protein | 878 | 67 | 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
- MTBC0 PGAP product: 'PadR family transcriptional regulator'
- Pfam: PadR PF03551 (E=3.5e-21) -- winged-helix-turn-helix repressor family
ESM Atlas signal (exploratory)
Ancestral protein hash 426716992f8cf5087fd0ef88029140fc ·
10 ESM-space neighbours (max similarity 0.919).
SAE features are orienting indices, not validated domains.
| # | Index | Activation | Interpretation |
|---|---|---|---|
| 1 | 6507 |
0.97 | HTH and winged-helix DNA-binding domains |
| 2 | 12403 |
0.81 | Amphipathic coiled-coil dimerization helices |
| 3 | 11889 |
0.69 | Post-HTH hinge helix |
| 4 | 14950 |
0.69 | N-terminal HTH DNA-binding core |
| 5 | 10186 |
0.65 | wHTH beta-hairpin wing |
| 6 | 9164 |
0.64 | Secondary-structure N-capping motifs |
| 7 | 2415 |
0.58 | Basic HTH DNA-recognition helices |
| 8 | 1235 |
0.57 | Glycine-rich nucleic-acid-binding loops |
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_214561.1)
- Domains: Pfam-A via hmmscan --cut_ga — PadR (PF03551.21)
- 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
COG1695 - Curated reference: UniProt P71704 (TrEMBL, unreviewed; 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
ino1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000052|Rv0047c| MLELAILGLLIESPMHGYELRKRLTGLLGAFRAFSYGSLYPALRRMQADGLIAENAAPAGTPVRRARRVYQLTDKGRRRFGELVADTGPHNYTDDGFGVHLAFFNRTPAEARMRILEGRRRQVEERREGLREAVARASSSFDRYTRQLHQLGLESSEREVKWLNELIAAERAAPNPAEQT