Rv3050c Family assigned · medium auto-curated
H37Rv Rv3050c · MTBC0 mtbc0_003242 ·
246 aa · 3432527–3433267 (-) ·
RefSeq NP_217566.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | AsnC family transcriptional regulator |
|---|---|
| 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 |
I6XG13
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulatory protein |
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.16% of strains (229) · 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 |
|---|---|---|---|---|
TetR_N | PF00440.30 | 6.5e-12 | 35–80 | Bacterial regulatory proteins, tetR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nrdI (NrdI protein), high confidence from genomic context alone (score 920 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3052c nrdI |
NrdI protein | 919 | 920 ctx | neighborhood:709 coexpression:735 |
Rv3051c nrdE |
ribonucleoside-diphosphate reductase subunit alpha | 889 | 890 ctx | neighborhood:557 coexpression:761 |
Rv3049c |
monooxygenase | 760 | 761 ctx | neighborhood:757 |
Rv3053c nrdH |
glutaredoxin electron transport protein NrdH | 755 | 756 ctx | neighborhood:625 |
Rv3048c nrdF2 |
ribonucleoside-diphosphate reductase subunit beta NrdF2 | 556 | 557 ctx | neighborhood:499 |
Rv0250c hyp |
hypothetical protein | 493 | 494 ctx | cooccurence:486 |
Rv0241c htdX |
3-hydroxyacyl-thioester dehydratase HtdX | 490 | 490 ctx | cooccurence:476 |
Rv0476 |
transmembrane protein | 472 | 472 | |
Rv0242c fabG4 |
3-oxoacyl-ACP reductase FabG | 469 | 469 ctx | cooccurence:459 |
Rv2138 lppL |
lipoprotein LppL | 463 | 464 ctx | cooccurence:461 |
Rv2743c hyp |
hypothetical protein | 441 | 441 ctx | cooccurence:424 |
Rv0243 fadA2 |
acetyl-CoA acetyltransferase FadA | 440 | 438 ctx | cooccurence:418 |
Rv2015c hyp |
hypothetical protein | 438 | 438 ctx | cooccurence:433 |
Rv0171 mce1C |
Mce family protein Mce1C | 431 | 432 ctx | cooccurence:428 |
Rv0431 |
tuberculin-like peptide | 411 | 411 |
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: AsnC family transcriptional regulator
- MTBC0 PGAP product: TetR/AcrR family transcriptional regulator
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=7e-12)
- (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_217566.1)
- 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 I6XG13 (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 —
28 functional partner(s); context anchor
nrdI - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003242|Rv3050c| MVRIPRPHPSAKPGVKVDARSERWREHRKKVRNEIVDAAFRAIDRLGPELSVRQIAEEAGTAKPKIYRHFTDKSDLLEAIGMRLRDMLWAAIFPSLDLATDSAREVIRRSVEEYVNLVDQHPNVLRVFIQGRSAKQSEATVRTLNEGREITLAMAEMFNNELREMELNRAALELAAFAAFGSAASATEWWLGPEPDSPRRMPREQFVAHLTTIMMGVIVGTAEALGIAVDPDQPIHDAVPNNPAVR