Rv3830c Family assigned · medium auto-curated
H37Rv Rv3830c · MTBC0 mtbc0_004059 ·
209 aa · 4329166–4329795 (-) ·
RefSeq NP_218347.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | TetR 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 |
P96248
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | tetR family |
| 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) pseudogene candidate
| pN/pS | 0.579 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 26.27% of strains (38152) · 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 | 9.8e-12 | 19–62 | Bacterial regulatory proteins, tetR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mftR (mycofactocin biosynthesis transcriptional regulator MftR), high confidence from genomic context alone (score 908 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 908 | 908 ctx | cooccurence:420 coexpression:848 |
Rv3167c |
TetR family transcriptional regulator | 934 | 896 | coexpression:860 |
Rv1359 |
transcriptional regulator | 890 | 891 | coexpression:827 |
Rv3829c |
dehydrogenase | 959 | 888 ctx | neighborhood:672 cooccurence:670 textmining:653 |
Rv3840 |
transcriptional regulator | 860 | 860 | coexpression:860 |
Rv1556 |
HTH-type transcriptional regulator | 863 | 859 | coexpression:802 |
Rv1931c |
transcriptional regulator | 862 | 858 | coexpression:836 |
Rv1776c |
transcriptional regulator | 861 | 858 | coexpression:804 |
Rv3124 moaR1 |
transcriptional regulator MoaR | 860 | 857 | coexpression:836 |
Rv1674c |
transcriptional regulator | 859 | 854 | coexpression:854 |
Rv2912c |
TetR family HTH-type transcriptional regulator | 852 | 847 | coexpression:796 |
Rv1267c embR |
transcriptional regulator EmbR | 849 | 846 | coexpression:824 |
Rv0117 oxyS |
oxidative stress response regulatory protein OxyS | 842 | 840 | coexpression:820 |
Rv2282c |
LysR family HTH-type transcriptional regulator | 836 | 834 | coexpression:813 |
Rv1151c cobB |
NAD-dependent protein deacylase | 839 | 833 | coexpression:833 |
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 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_218347.1)
- 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 P96248 (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 —
99 functional partner(s); context anchor
mftR - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004059|Rv3830c| MVRPPQTARSERTREALRQAALVRFLAQGVEATSAEQIAEDAGVSLRTFYRHFRSKHDLLFADYDAGLHWFRAALDARPADESIIDSVQAAIFSFPYDVDAVTKIASLRRGELEPSRIVRHMREVEADFADAIQAQLRRRNCDIAGAPDARLHIAVTARCVAAAVFGAMEAWMLGSDRSLGELARVCHVALESLRVGISDTWTTLTVSS