mce2R Family assigned · medium auto-curated
H37Rv Rv0586 · MTBC0 mtbc0_000616 ·
240 aa · 687961–688683 (+) ·
RefSeq NP_215100.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator Mce2R |
|---|---|
| MTBC0 PGAP re-annotation | FadR family transcriptional regulator Mce2R |
| Revised (this work) | FadR family transcriptional regulator Mce2R. Pfam: GntR (PF00392.28), FCD (PF07729.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMG5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH-type transcriptional regulator Mce2R |
| Curated function | Negatively regulates the expression of its operon as well as expression of end (endonuclease 4). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | mce2R |
| eggNOG description | GntR family |
| Orthologous group | COG2186 |
| Gene Ontology (59) |
GO:0003674, GO:0003676, GO:0003677, GO:0005488, GO:0005575, GO:0006355, GO:0008150, GO:0009605, GO:0009607, GO:0009889, GO:0009890, GO:0009892 +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 | 1.054 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.14% of strains (197) · 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 |
|---|---|---|---|---|
GntR | PF00392.28 | 8.6e-20 | 13–74 | Bacterial regulatory proteins, gntR family |
FCD | PF07729.18 | 6.9e-10 | 113–223 | FCD domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mce2C (Mce family protein Mce2C), high confidence from genomic context alone (score 803 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0587 yrbE2A hyp |
hypothetical protein | 985 | 889 ctx | neighborhood:882 textmining:870 |
Rv0588 yrbE2B hyp |
hypothetical protein | 958 | 886 ctx | neighborhood:882 textmining:653 |
Rv0591 mce2C |
Mce family protein Mce2C | 803 | 803 ctx | neighborhood:801 |
Rv0589 mce2A |
Mce family protein Mce2A | 957 | 789 ctx | neighborhood:786 textmining:805 |
Rv0590 mce2B |
Mce-family protein Mce2B; Rv0590, (MTCY19H5.32c), len: 275 aa. Mce2B; belongs to 24-membered Mycobacterium tuberculosis Mce protein family ( | 788 | 787 ctx | neighborhood:785 |
Rv0590A |
Mce-family related protein; Rv0590A, len: 84 aa. Probable continuation of mce2B|Rv0590. Can find no frameshift to account for this. Possible | 787 | 786 ctx | neighborhood:785 |
Rv0594 mce2F |
Mce family protein Mce2F | 820 | 782 ctx | neighborhood:781 |
Rv0593 lprL |
Mce family lipoprotein LprL | 782 | 782 ctx | neighborhood:781 |
Rv0592 mce2D |
Mce family protein Mce2D | 782 | 782 ctx | neighborhood:781 |
Rv0585c |
integral membrane protein | 566 | 545 ctx | neighborhood:545 |
Rv0792c |
transcriptional regulator | 534 | 516 | |
Rv0043c |
HTH-type transcriptional regulator | 561 | 503 ctx | cooccurence:469 |
Rv0904c accD3 |
acetyl-CoAcarboxylase carboxyl transferase subunit beta | 542 | 503 | coexpression:431 |
Rv0165c mce1R |
transcriptional regulator Mce1R | 829 | 456 ctx | cooccurence:416 textmining:700 |
Rv1719 |
transcriptional regulator | 429 | 399 |
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 Mce2R
- MTBC0 PGAP product: FadR family transcriptional regulator Mce2R
- Pfam (hmmscan --cut_ga): GntR PF00392.28 (E=9e-20), FCD PF07729.18 (E=7e-10)
- (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_215100.1)
- Domains: Pfam-A via hmmscan --cut_ga — GntR (PF00392.28), FCD (PF07729.18)
- 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
COG2186 - Curated reference: UniProt P9WMG5 (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 —
21 functional partner(s); context anchor
mce2C - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000616|Rv0586|mce2R MALQPVTRRSVPEEVFEQIATDVLTGEMPPGEALPSERRLAELLGVSRPAVREALKRLSAAGLVEVRQGDVTTVRDFRRHAGLDLLPRLLFRNGELDISVVRSILEARLRNFPKVAELAAERNEPELAELLQDSLRALDTEEDPIVWQRHTLDFWDHVVDSAGSIVDRLMYNAFRAAYEPTLAALTTTMTAAAKRPSDYRKLADAICSGDPTGAKKAAQDLLELANTSLMAVLVSQASRQ