mmpR5 Family assigned · medium auto-curated
H37Rv Rv0678 · MTBC0 mtbc0_000717 ·
165 aa · 783076–783573 (+) ·
RefSeq NP_215192.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | siderophore transport transcriptional regulator MmpR5 |
| Revised (this work) | Siderophore transport transcriptional regulator MmpR5. Pfam: HTH_MmpR5 (PF27059.1). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y8F7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH-type transcriptional regulator MmpR5 |
| Curated function | Controls the expression level of the Mmps2-MmpL2, MmpS4-MmpL4, and MmpS5-MmpL5 transport systems. Also controls its own expression. Acts by binding directly to the promoter regions. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | regulation of RNA biosynthetic process |
| Orthologous group | COG1510 |
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, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.16% of strains (234) · 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 |
|---|---|---|---|---|
HTH_MmpR5 | PF27059.1 | 7.0e-15 | 98–159 | MmpR5-like MarR family transcriptional regulator |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mmpL5 (transmembrane transport protein MmpL5), high confidence from genomic context alone (score 915 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0676c mmpL5 |
transmembrane transport protein MmpL5 | 989 | 915 ctx | neighborhood:571 coexpression:810 textmining:883 |
Rv0677c mmpS5 |
membrane protein MmpS5 | 974 | 814 ctx | neighborhood:601 coexpression:553 textmining:870 |
Rv3160c |
TetR family transcriptional regulator | 799 | 799 | coexpression:799 |
Rv3066 |
DeoR family transcriptional regulator | 812 | 773 | coexpression:739 |
Rv1152 |
transcriptional regulator | 580 | 580 | coexpression:580 |
Rv0792c |
transcriptional regulator | 474 | 474 | coexpression:474 |
Rv1733c |
transmembrane protein | 426 | 426 ctx | cooccurence:423 |
Rv1404 |
transcriptional regulator | 474 | 326 | |
Rv1455 hyp |
hypothetical protein | 416 | 234 | |
Rv3855 ethR |
HTH-type transcriptional repressor EthR | 442 | 212 | |
Rv1453 |
transcriptional activator protein | 533 | 85 | textmining:511 |
Rv1049 |
transcriptional repressor | 811 | 80 | textmining:803 |
Rv0880 |
HTH-type transcriptional regulator | 559 | 65 | textmining:548 |
Rv2043c pncA |
pyrazinamidase/nicotinamidase PncA | 572 | 64 | textmining:562 |
Rv1173 fbiC |
FO synthase | 663 | 58 | textmining:657 |
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: hypothetical protein
- MTBC0 PGAP product: siderophore transport transcriptional regulator MmpR5
- Pfam (hmmscan --cut_ga): HTH_MmpR5 PF27059.1 (E=7e-15)
- (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_215192.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_MmpR5 (PF27059.1)
- 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
COG1510 - Curated reference: UniProt I6Y8F7 (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 —
30 functional partner(s); context anchor
mmpL5 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000717|Rv0678|mmpR5 MSVNDGVDQMGAEPDIMEFVEQMGGYFESRSLTRLAGRLLGWLLVCDPERQSSEELATALAASSGGISTNARMLIQFGFIERLAVAGDRRTYFRLRPNAFAAGERERIRAMAELQDLADVGLRALGDAPPQRSRRLREMRDLLAYMENVVSDALGRYSQRTGEDD