Rv2250c Family assigned · medium auto-curated
H37Rv Rv2250c · MTBC0 mtbc0_002392 ·
189 aa · 2550946–2551515 (-) ·
RefSeq NP_216766.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type 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 |
P9WMC5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized HTH-type transcriptional regulator Rv2250c |
UniProt still lists this protein as Uncharacterized HTH-type transcriptional regulator Rv2250c; 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 |
| Gene Ontology (41) |
GO:0000976, GO:0001067, GO:0003674, GO:0003676, GO:0003677, GO:0003690, GO:0003700, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737 +29 more
|
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 | 0.363 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
TetR_N | PF00440.30 | 1.0e-11 | 15–58 | Bacterial regulatory proteins, tetR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: glpD1 (glycerol-3-phosphate dehydrogenase), high confidence from genomic context alone (score 930 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2249c glpD1 |
glycerol-3-phosphate dehydrogenase | 930 | 930 ctx | neighborhood:882 |
Rv2250A |
Possible flavoprotein; Rv2250A, len: 139 aa. Conserved hypothetical protein, possibly flavoprotein. Similar to N-terminus of SCF91.28c|AL132 | 890 | 890 ctx | neighborhood:600 cooccurence:727 |
Rv2252 dagK |
diacylglycerol kinase | 798 | 799 ctx | neighborhood:743 |
Rv2251 |
flavoprotein | 794 | 794 ctx | neighborhood:600 cooccurence:480 |
Rv0330c hyp |
hypothetical protein | 733 | 733 | coexpression:733 |
Rv2253 hyp |
hypothetical protein | 596 | 597 ctx | neighborhood:594 |
Rv3830c |
TetR family transcriptional regulator | 491 | 476 ctx | cooccurence:450 |
Rv0767c |
HTH-type transcriptional regulator | 437 | 438 | |
Rv0275c |
transcriptional regulator | 587 | 416 ctx | cooccurence:408 |
Rv1776c |
transcriptional regulator | 410 | 410 | |
Rv2991 hyp |
hypothetical protein | 405 | 405 | |
Rv0494 |
HTH-type transcriptional regulator | 421 | 404 | coexpression:403 |
Rv1014c pth |
peptidyl-tRNA hydrolase | 400 | 401 | |
Rv0825c hyp |
hypothetical protein | 400 | 400 ctx | cooccurence:400 |
Rv3066 |
DeoR family transcriptional regulator | 486 | 378 |
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: TetR/AcrR family transcriptional regulator
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=1e-11)
- (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_216766.2)
- 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 P9WMC5 (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 —
20 functional partner(s); context anchor
glpD1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002392|Rv2250c| MLSMSNDRADTGGRILRAAASCVVDYGVDRVTLAEIARRAGVSRPTVYRRWPDTRSIMASMLTSHIADVLREVPLDGDDREALVKQIVAVADRLRGDDLIMSVMHSELARVYITERLGTSQQVLIEGLAARLTVAQRSGSVRSGDARRLATMVLLIAQSTIQSADIVDSILDSAALATELTHALNGYLC