mce1R Family assigned · medium auto-curated
H37Rv Rv0165c · MTBC0 - ·
223 aa · 194144–194815 (-) ·
RefSeq YP_177700.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator Mce1R |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transcriptional regulator Mce1R. 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.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
Q79G00
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulatory protein Mce1R |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | GntR family |
| Orthologous group | COG1802 |
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 | 0.243 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 62.13% of strains (90217) · reference-fixed |
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 | 3.2e-13 | 20–82 | Bacterial regulatory proteins, gntR family |
FCD | PF07729.18 | 1.8e-07 | 92–182 | FCD domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadD5 (fatty-acid--CoA ligase FadD5), medium confidence from genomic context alone (score 614 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0166 fadD5 |
fatty-acid--CoA ligase FadD5 | 803 | 614 ctx | neighborhood:524 textmining:513 |
Rv3002c ilvN |
acetolactate synthase small subunit | 571 | 571 | coexpression:469 |
Rv3060c |
GntR family transcriptional regulator | 595 | 542 ctx | cooccurence:501 |
Rv1773c |
transcriptional regulator | 525 | 507 ctx | cooccurence:472 |
Rv1719 |
transcriptional regulator | 498 | 479 ctx | cooccurence:456 |
Rv0494 |
HTH-type transcriptional regulator | 527 | 465 ctx | cooccurence:420 |
Rv0167 yrbE1A |
membrane protein | 520 | 460 | |
Rv0586 mce2R |
HTH-type transcriptional regulator Mce2R | 829 | 456 ctx | cooccurence:416 textmining:700 |
Rv0171 mce1C |
Mce family protein Mce1C | 455 | 455 | |
Rv0172 mce1D |
Mce family protein Mce1D | 523 | 441 | |
Rv1200 |
integral membrane transport protein | 448 | 428 | coexpression:412 |
Rv1300 hemK |
release factor glutamine methyltransferase | 427 | 428 | experimental:409 |
Rv0169 mce1A |
Mce family protein Mce1A | 911 | 388 | textmining:861 |
Rv0792c |
transcriptional regulator | 444 | 373 | |
Rv0168 yrbE1B |
membrane protein | 463 | 353 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): transcriptional regulator Mce1R
- Pfam (hmmscan --cut_ga): GntR PF00392.28 (E=3e-13), FCD PF07729.18 (E=2e-07)
- (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 YP_177700.2)
- 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
COG1802 - Curated reference: UniProt Q79G00 (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 —
22 functional partner(s); context anchor
fadD5 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0165c|mce1R MNAPLSAKPRSQLPLRRAQLSDEVAGHLRAAIMSGALRSGTFIRLDETAAELGVSVTPVREALLKLRGEGMVGLEPHRGHVVLPLTRQDIDDIFWLQATIAQELATSATAHITDVEIDELDRINNALAGAIGSGDAKTIASIEFAFHRVFNKASRRIKLAWFLLNAARYMGAGVRGRPAMGRGRGEQSSAADRRAAPPRHSRRNRAHRLAVHRWGTQADGGPG