Rv2912c Family assigned · medium auto-curated
H37Rv Rv2912c · MTBC0 mtbc0_003094 ·
195 aa · 3240103–3240690 (-) ·
RefSeq NP_217428.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | TetR family 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 |
P9WMC7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized HTH-type transcriptional regulator Rv2912c |
UniProt still lists this protein as Uncharacterized HTH-type transcriptional regulator Rv2912c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Bacterial regulatory proteins, tetR family |
| 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 | 1.055 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 | 2.4e-08 | 16–61 | Bacterial regulatory proteins, tetR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2913c (D-amino acid aminohydrolase), high confidence from genomic context alone (score 922 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2913c |
D-amino acid aminohydrolase | 972 | 922 ctx | neighborhood:881 textmining:653 |
Rv3830c |
TetR family transcriptional regulator | 852 | 847 | coexpression:796 |
Rv0452 |
transcriptional regulator | 842 | 842 ctx | cooccurence:434 coexpression:733 |
Rv3833 |
AraC family transcriptional regulator | 829 | 821 | coexpression:817 |
Rv3082c virS |
HTH-type transcriptional regulator VirS | 824 | 805 | coexpression:805 |
Rv3736 |
AraC/XylS family transcriptional regulator | 805 | 802 | coexpression:802 |
Rv1151c cobB |
NAD-dependent protein deacylase | 808 | 801 | coexpression:801 |
Rv3167c |
TetR family transcriptional regulator | 800 | 800 | coexpression:800 |
Rv0792c |
transcriptional regulator | 805 | 798 | coexpression:798 |
Rv3840 |
transcriptional regulator | 798 | 798 | coexpression:798 |
Rv1963c mce3R |
transcriptional repressor Mce3R | 792 | 793 | coexpression:751 |
Rv1167c |
transcriptional regulator | 791 | 791 | coexpression:791 |
Rv0767c |
HTH-type transcriptional regulator | 776 | 777 | coexpression:733 |
Rv1931c |
transcriptional regulator | 765 | 766 | coexpression:733 |
Rv1985c lysG |
HTH-type transcriptional regulator | 767 | 763 | coexpression:734 |
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: TetR family HTH-type transcriptional regulator
- MTBC0 PGAP product: TetR/AcrR family transcriptional regulator
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=2e-08)
- (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_217428.1)
- 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 P9WMC7 (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 —
75 functional partner(s); context anchor
Rv2913c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003094|Rv2912c| MARTQQQRREETVARLLQASIDTIIEVGYARASAAVITKRAGVSVGALFRHFETMGDFMAATAYEVLRRQLETFTKQVAEIPADRPALPAALTILRDITAGSTNAVLYELMVAARTDEKLKETLQNVLGQYSAKIHDAARALPGAESFPEETFPVIVALMTNVFDGAAIVRGVLPQPELEEQRIPMLTALLTAGL