Rv0825c Family assigned · medium auto-curated
H37Rv Rv0825c · MTBC0 mtbc0_000874 ·
213 aa · 921979–922620 (-) ·
RefSeq NP_215340.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | TetR/AcrR family transcriptional regulator |
| Revised (this work) | TetR/AcrR family transcriptional regulator. Pfam: TetR_N (PF00440.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53836
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 | COG1309 |
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 | 1.289 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 11 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 |
|---|---|---|---|---|
TetR_N | PF00440.30 | 2.6e-05 | 26–72 | Bacterial regulatory proteins, tetR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: desA1 (acyl-ACP desaturase DesA), high confidence from genomic context alone (score 748 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) |
|---|---|---|---|---|
Rv0826 hyp |
hypothetical protein | 916 | 916 ctx | neighborhood:783 cooccurence:629 |
Rv0824c desA1 |
acyl-ACP desaturase DesA | 748 | 748 ctx | neighborhood:747 |
Rv0823c dusB |
tRNA-dihydrouridine synthase | 691 | 691 ctx | neighborhood:690 |
Rv1645c hyp |
hypothetical protein | 654 | 655 ctx | cooccurence:652 |
Rv0276 hyp |
hypothetical protein | 623 | 623 ctx | cooccurence:572 |
Rv2237 hyp |
hypothetical protein | 622 | 622 ctx | cooccurence:569 |
Rv3740c |
diacyglycerol O-acyltransferase | 600 | 600 ctx | cooccurence:594 |
Rv3734c tgs2 |
diacyglycerol O-acyltransferase | 598 | 599 ctx | cooccurence:592 |
Rv2743c hyp |
hypothetical protein | 543 | 543 ctx | cooccurence:542 |
Rv0822c hyp |
hypothetical protein | 533 | 533 ctx | neighborhood:532 |
Rv0895 |
diacyglycerol O-acyltransferase | 504 | 504 ctx | cooccurence:499 |
Rv0945 |
oxidoreductase | 475 | 475 ctx | cooccurence:474 |
Rv3391 acrA1 |
acyl-CoA-reductase AcrA | 467 | 467 ctx | cooccurence:459 |
Rv3480c |
diacyglycerol O-acyltransferase | 446 | 447 ctx | cooccurence:444 |
Rv2912c |
TetR family HTH-type transcriptional regulator | 441 | 442 ctx | cooccurence:440 |
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: hypothetical protein
- MTBC0 PGAP product: TetR/AcrR family transcriptional regulator
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=3e-05)
- (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_215340.1)
- Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30)
- 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
COG1309 - Curated reference: UniProt O53836 (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
desA1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000874|Rv0825c| MQTGQNRGRWSGVPLESRHALRRDNLVAAGVQLLGGAGGPALTVRAVCRHAGLTERYFYESFADREHFVRAVYDDVCTRAMATLTSAQTPREAVEQFVELMVDDPVRGRVLLLAPAVEPALTRSGAEWMPNFIELLQRKLSRIVDPVLQKLVATSLIGALTGLFTAYLNGRLGATRKQFIDYCVNMLLSTAATYAPHRERGESEHSIPAGPHN