Rv3405c Family assigned · medium auto-curated
H37Rv Rv3405c · MTBC0 mtbc0_003619 ·
188 aa · 3850141–3850707 (-) ·
RefSeq NP_217922.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | helix-turn-helix domain-containing protein |
| Revised (this work) | Helix-turn-helix domain-containing protein. 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 |
P9WMC3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH-type transcriptional repressor Rv3405c |
| Curated function | Negatively regulates the expression of sulfate ester dioxygenase Rv3406 and its own expression. Binds specifically to the inverted repeat sequence of the intergenic region between Rv3405c and Rv3406. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | transcriptional |
| Orthologous group | COG1309 |
| KEGG orthology |
K22295
|
| 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 | 1.9e-16 | 23–69 | Bacterial regulatory proteins, tetR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3406 (dioxygenase), high confidence from genomic context alone (score 786 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1151c cobB |
NAD-dependent protein deacylase | 806 | 799 | coexpression:799 |
Rv3406 |
dioxygenase | 971 | 786 ctx | neighborhood:786 textmining:870 |
Rv3183 higA3 |
transcriptional regulator | 767 | 767 | coexpression:767 |
Rv2282c |
LysR family HTH-type transcriptional regulator | 764 | 761 | coexpression:731 |
Rv3066 |
DeoR family transcriptional regulator | 740 | 740 | coexpression:740 |
Rv3840 |
transcriptional regulator | 738 | 738 | coexpression:738 |
Rv3488 hyp |
hypothetical protein | 738 | 734 | coexpression:734 |
Rv1960c parD1 |
antitoxin ParD1 | 734 | 734 | coexpression:734 |
Rv0494 |
HTH-type transcriptional regulator | 740 | 733 | coexpression:732 |
Rv0603 hyp |
hypothetical protein | 733 | 733 | coexpression:733 |
Rv3830c |
TetR family transcriptional regulator | 730 | 730 | coexpression:730 |
Rv3736 |
AraC/XylS family transcriptional regulator | 733 | 729 | coexpression:729 |
Rv1027c kdpE |
transcriptional regulator KdpE | 716 | 716 | coexpression:716 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 703 | 703 | coexpression:703 |
Rv3291c lrpA |
transcriptional regulator LrpA | 696 | 687 | coexpression:687 |
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: helix-turn-helix domain-containing protein
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=2e-16)
- (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_217922.1)
- 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 P9WMC3 (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 —
41 functional partner(s); context anchor
Rv3406 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003619|Rv3405c| MTTRPATDRRKMPTGREEVAAAILQAATDLFAERGPAATSIRDIAARSKVNHGLVFRHFGTKDQLVGAVLDHLGTKLTRLLHSEAPADIIERALDRHGRVLARALLDGYPVGQLQQRFPNVAELLDAVRPRYDSDLGARLAVAHALALQFGWRLFAPMLRSATGIDELTGDELRLSVNDAVARILEPH