Rv1473A Family assigned · medium auto-curated
H37Rv Rv1473A · MTBC0 - ·
63 aa · 1662381–1662572 (+) ·
RefSeq YP_177644.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transcriptional regulator. Pfam: HTH_58 (PF19575.6). |
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 |
L7N691
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | transcriptional regulator |
| Orthologous group | 2E4I7 |
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) pseudogene candidate
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 1.35% of strains (1956) · clonal |
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_58 | PF19575.6 | 2.7e-21 | 6–58 | Helix-turn-helix domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1473 (macrolide ABC transporter ATP-binding protein), high confidence from genomic context alone (score 940 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1473 |
macrolide ABC transporter ATP-binding protein | 940 | 940 ctx | neighborhood:774 coexpression:746 |
Rv1472 echA12 |
enoyl-CoA hydratase EchA12 | 745 | 745 ctx | neighborhood:741 |
Rv2314c hyp |
hypothetical protein | 606 | 606 ctx | cooccurence:606 |
Rv3287c rsbW |
anti-sigma factor RsbW | 578 | 579 ctx | cooccurence:576 |
Rv2709 |
transmembrane protein | 551 | 552 ctx | cooccurence:549 |
Rv2844 hyp |
hypothetical protein | 546 | 546 ctx | cooccurence:541 |
Rv3662c hyp |
hypothetical protein | 541 | 541 ctx | cooccurence:540 |
Rv2315c hyp |
hypothetical protein | 531 | 531 ctx | cooccurence:531 |
Rv3231c hyp |
hypothetical protein | 510 | 510 ctx | cooccurence:488 |
Rv2170 |
GCN5-like N-acetyltransferase | 478 | 479 ctx | cooccurence:477 |
Rv2912c |
TetR family HTH-type transcriptional regulator | 469 | 469 | |
Rv3118 sseC1 hyp |
hypothetical protein | 469 | 469 ctx | cooccurence:456 |
Rv0546c hyp |
hypothetical protein | 467 | 467 ctx | cooccurence:467 |
Rv1471 trxB1 |
thioredoxin | 463 | 463 ctx | neighborhood:460 |
Rv0814c sseC2 hyp |
hypothetical protein | 458 | 459 ctx | cooccurence:456 |
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): transcriptional regulator
- Pfam (hmmscan --cut_ga): HTH_58 PF19575.6 (E=3e-21)
- (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 YP_177644.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_58 (PF19575.6)
- 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
2E4I7 - Curated reference: UniProt L7N691 (TrEMBL, unreviewed; Predicted)
- 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 —
24 functional partner(s); context anchor
Rv1473 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1473A| MRKSKKTRDQLLRELRNAYEGGASIRNLAATTGRSYGSIHSMLRESGTTMRGRGGPNRRSRPR