mce3R Family assigned · medium auto-curated
H37Rv Rv1963c · MTBC0 mtbc0_002079 ·
406 aa · 2224698–2225918 (-) ·
RefSeq NP_216479.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional repressor Mce3R |
|---|---|
| MTBC0 PGAP re-annotation | TetR family transcriptional regulator Mce3R |
| Revised (this work) | TetR family transcriptional regulator Mce3R. 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 |
P95251
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Transcriptional repressor Mce3R |
| Curated function | Mce3R represses the transcription of mce3 operon and down-regulates its own expression, but does not affect the transcription of mce1, mce2 and mce4 operons. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | mce3R |
| eggNOG description | Regulatory |
| Orthologous group | COG1309 |
| Gene Ontology (59) |
GO:0000976, GO:0001067, GO:0003674, GO:0003676, GO:0003677, GO:0003690, GO:0003700, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737 +47 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 | 0.442 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 5 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 | 7.2e-17 | 19–65 | Bacterial regulatory proteins, tetR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: iniR (transcriptional regulator), high confidence from genomic context alone (score 891 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0339c iniR |
transcriptional regulator | 891 | 891 ctx | cooccurence:608 coexpression:734 |
Rv1267c embR |
transcriptional regulator EmbR | 870 | 868 | coexpression:815 |
Rv0452 |
transcriptional regulator | 826 | 826 | coexpression:826 |
Rv1931c |
transcriptional regulator | 803 | 803 | coexpression:803 |
Rv0212c nadR |
transcriptional regulator NadR | 810 | 801 | coexpression:801 |
Rv3167c |
TetR family transcriptional regulator | 800 | 800 | coexpression:800 |
Rv3830c |
TetR family transcriptional regulator | 804 | 799 | coexpression:799 |
Rv3082c virS |
HTH-type transcriptional regulator VirS | 802 | 799 | coexpression:799 |
Rv1027c kdpE |
transcriptional regulator KdpE | 799 | 798 | coexpression:798 |
Rv2912c |
TetR family HTH-type transcriptional regulator | 792 | 793 | coexpression:751 |
Rv0494 |
HTH-type transcriptional regulator | 797 | 791 | coexpression:737 |
Rv1674c |
transcriptional regulator | 793 | 785 | coexpression:785 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 783 | 783 | coexpression:783 |
Rv1151c cobB |
NAD-dependent protein deacylase | 784 | 776 | coexpression:776 |
Rv2282c |
LysR family HTH-type transcriptional regulator | 814 | 769 | coexpression:740 |
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: transcriptional repressor Mce3R
- MTBC0 PGAP product: TetR family transcriptional regulator Mce3R
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=7e-17)
- (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_216479.1)
- 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 P95251 (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 —
86 functional partner(s); context anchor
iniR - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002079|Rv1963c|mce3R MASVAQPVRRRPKDRKKQILDQAVGLFIERGFHSVKLEDIAEAAGVTARALYRHYDNKQALLAEAIRTGQDQYQSARRLTEGETEPTPRPLNADLEDLIAAAVASRALTVLWQREARYLNEDDRTAVRRRINAIVAGMRDSVLLEVPDLSPQHSELRAWAVSSTLTSLGRHSLSLPGEELKKLLYQACMAAARTPPVCELPPLPAGDAARDEADVLFSRYETLLAAGARLFRAQGYPAVNTSEIGKGAGIAGPGLYRSFSSKQAILDALIRRLDEWRCLECIRALRANQQAAQRLRGLVQGHVRISLDAPDLVAVSVTELSHASVEVRDGYLRNQGDREAVWIDLIGKLVPATSVAQGRLLVAAAISFIEDVARTWHLTRYAGVADEISGLALAILTSGAGNLLRA