cmr Family assigned · medium auto-curated
H37Rv Rv1675c · MTBC0 mtbc0_001783 ·
244 aa · 1912256–1912990 (-) ·
RefSeq NP_216191.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator Cmr |
|---|---|
| MTBC0 PGAP re-annotation | HTH-type transcriptional regulator Cmr |
| Revised (this work) | HTH-type transcriptional regulator Cmr. Pfam: cNMP_binding (PF00027.36), HTH_Crp_2 (PF13545.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMH5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH-type transcriptional regulator Cmr |
| Curated function | Positively regulates the expression of at least groEL2. Cyclic AMP does not affect transcription in vitro. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | transcriptional |
| Orthologous group | COG0664 |
| KEGG orthology |
K21884
|
| Gene Ontology (25) |
GO:0003674, GO:0003676, GO:0003677, GO:0005488, GO:0006355, GO:0008150, GO:0009889, GO:0010468, GO:0010556, GO:0019219, GO:0019222, GO:0031323 +13 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 | 1.448 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.17% of strains (248) · 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 |
|---|---|---|---|---|
cNMP_binding | PF00027.36 | 1.8e-19 | 60–146 | Cyclic nucleotide-binding domain |
HTH_Crp_2 | PF13545.13 | 3.9e-11 | 179–241 | Crp-like helix-turn-helix domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1674c (transcriptional regulator), high confidence from genomic context alone (score 903 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2488c |
LuxR family transcriptional regulator | 935 | 932 | coexpression:856 experimental:440 |
Rv1674c |
transcriptional regulator | 918 | 903 ctx | neighborhood:420 coexpression:839 |
Rv1359 |
transcriptional regulator | 898 | 895 | coexpression:833 |
Rv0602c tcrA |
two component DNA binding transcriptional regulator TcrA | 877 | 870 | coexpression:854 |
Rv1189 sigI |
ECF RNA polymerase sigma factor SigI | 870 | 865 | coexpression:845 |
Rv2282c |
LysR family HTH-type transcriptional regulator | 869 | 862 | coexpression:862 |
Rv3736 |
AraC/XylS family transcriptional regulator | 865 | 860 | coexpression:860 |
Rv1931c |
transcriptional regulator | 861 | 860 | coexpression:860 |
Rv3840 |
transcriptional regulator | 860 | 860 | coexpression:860 |
Rv1267c embR |
transcriptional regulator EmbR | 860 | 860 | coexpression:860 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 860 | 860 | coexpression:860 |
Rv3167c |
TetR family transcriptional regulator | 859 | 859 | coexpression:859 |
Rv1190 hyp |
hypothetical protein | 851 | 851 | coexpression:850 |
Rv0603 hyp |
hypothetical protein | 850 | 850 | coexpression:850 |
Rv3263 |
DNA methylase | 848 | 848 | coexpression:848 |
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 Cmr
- MTBC0 PGAP product: HTH-type transcriptional regulator Cmr
- Pfam (hmmscan --cut_ga): cNMP_binding PF00027.36 (E=2e-19), HTH_Crp_2 PF13545.13 (E=4e-11)
- (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_216191.1)
- Domains: Pfam-A via hmmscan --cut_ga — cNMP_binding (PF00027.36), HTH_Crp_2 (PF13545.13)
- 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
COG0664 - Curated reference: UniProt P9WMH5 (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 —
161 functional partner(s); context anchor
Rv1674c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001783|Rv1675c|cmr MADRSVRPLRHLVHAVTGGQPPSEAQVRQAAWIARCVGRGGSAPLHRDDVSALAETLQAKEFAPGAVVFHADQTADGVWIVRHGLIELAVGSRRRRAVVNILHPGDVDGDIPLLLEMPMVYTGRALTQATCLFLDRQAFERLLATHPAIARRWLSSVAQRVSTAQIRLMGMLGRPLPAQVAQLLLDEAIDARIELAQRTLAAMLGAQRPSINKILKEFERDRLITVGYAVIEITDQHGLRARAQ