csoR Resolved · high auto-curated
H37Rv Rv0967 · MTBC0 mtbc0_001033 ·
119 aa · 1085190–1085549 (+) ·
RefSeq NP_215482.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | copper-sensing transcriptional repressor CsoR |
|---|---|
| MTBC0 PGAP re-annotation | copper-sensing transcriptional repressor CsoR |
| Revised (this work) | Copper-sensing transcriptional repressor CsoR. Pfam: Trns_repr_metal (PF02583.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WP49
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Copper-sensing transcriptional repressor CsoR |
| Curated function | Copper-sensitive repressor that has a key role in copper homeostasis. It is part of the cso operon involved in the cellular response to increasing concentrations of copper inside the bacterium, which can be highly toxic. In the presence of copper, CsoR fully dissociates from the promoter in the cso operon, leading to the transcription of its genes. Binds to a GC-rich pseudopallindromic sequence, 5'-GTAGCCCACCCCCAGTGGGGTGGGA-3', in the cso promoter region. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | csoR |
| eggNOG description | Copper-sensitive repressor that has a key role in copper homeostasis. It is part of the cso operon involved in the cellular response to increasing concentrations of copper inside the bacterium, which can be highly toxic. In the presence of copper, CsoR fully dissociates from the promoter in the cso operon, leading to the transcription of its genes. Binds to a GC-rich pseudopallindromic sequence, 5'-GTAGCCCACCCCCAGTGGGGTGGGA-3', in the cso promoter region |
| Orthologous group | COG1937 |
| KEGG orthology |
K21600
|
| Gene Ontology (71) |
GO:0000976, GO:0001067, GO:0001130, GO:0001217, GO:0003674, GO:0003676, GO:0003677, GO:0003690, GO:0003700, GO:0005488, GO:0005507, GO:0005575 +59 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 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 |
|---|---|---|---|---|
Trns_repr_metal | PF02583.23 | 1.3e-24 | 9–87 | Metal-sensitive transcriptional repressor |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ctpV (copper-exporting ATPase), medium confidence from genomic context alone (score 662 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0968 hyp |
hypothetical protein | 968 | 845 ctx | neighborhood:647 coexpression:580 textmining:803 |
Rv1766 hyp |
hypothetical protein | 873 | 733 ctx | cooccurence:733 textmining:545 |
Rv0969 ctpV |
copper-exporting ATPase | 936 | 662 ctx | neighborhood:490 textmining:820 |
Rv0966c hyp |
hypothetical protein | 578 | 578 ctx | neighborhood:574 |
Rv0970 |
integral membrane protein | 940 | 564 ctx | neighborhood:538 textmining:870 |
Rv0965c hyp |
hypothetical protein | 488 | 488 ctx | neighborhood:488 |
Rv3086 adhD |
alcohol dehydrogenase D | 472 | 451 | coexpression:432 |
Rv0162c adhE1 |
zinc-type alcohol dehydrogenase subunit E | 469 | 448 | coexpression:429 |
Rv2259 mscR |
S-nitrosomycothiol reductase MscR | 469 | 448 | coexpression:429 |
Rv0761c adhB |
alcohol dehydrogenase B | 469 | 448 | coexpression:429 |
Rv0129c fbpC |
diacylglycerol acyltransferase/mycolyltransferase Ag85C | 449 | 429 | coexpression:411 |
Rv1639c hyp |
hypothetical protein | 449 | 428 | coexpression:410 |
Rv1288 hyp |
hypothetical protein | 455 | 427 | coexpression:409 |
Rv3803c fbpD |
MPT51/MPB51 antigen | 448 | 427 | coexpression:409 |
Rv3804c fbpA |
diacylglycerol acyltransferase/mycolyltransferase Ag85A | 448 | 427 | coexpression:409 |
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: copper-sensing transcriptional repressor CsoR
- MTBC0 PGAP product: copper-sensing transcriptional repressor CsoR
- Pfam (hmmscan --cut_ga): Trns_repr_metal PF02583.23 (E=1e-24)
- (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_215482.1)
- Domains: Pfam-A via hmmscan --cut_ga — Trns_repr_metal (PF02583.23)
- 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
COG1937 - Curated reference: UniProt P9WP49 (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 —
31 functional partner(s); context anchor
ctpV - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001033|Rv0967|csoR MSKELTAKKRAALNRLKTVRGHLDGIVRMLESDAYCVDVMKQISAVQSSLERANRVMLHNHLETCFSTAVLDGHGQAAIEELIDAVKFTPALTGPHARLGGAAVGESATEEPMPDASNM