crcB Resolved · high auto-curated
H37Rv Rv3069 · MTBC0 mtbc0_003262 ·
132 aa · 3455056–3455454 (+) ·
RefSeq NP_217585.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | fluoride ion transporter CrcB |
|---|---|
| MTBC0 PGAP re-annotation | fluoride efflux transporter CrcB |
| Revised (this work) | Fluoride efflux transporter CrcB. Pfam: CRCB (PF02537.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WP63
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Fluoride-specific ion channel FluC 1 |
| Curated function | Fluoride-specific ion channel. Important for reducing fluoride concentration in the cell, thus reducing its toxicity. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| Preferred name | crcB |
| eggNOG description | Important for reducing fluoride concentration in the cell, thus reducing its toxicity |
| Orthologous group | COG0239 |
| KEGG orthology |
K06199
|
| Gene Ontology (33) |
GO:0003674, GO:0005215, GO:0005575, GO:0005623, GO:0005886, GO:0005887, GO:0006810, GO:0006811, GO:0006820, GO:0008150, GO:0008509, GO:0015075 +21 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 | 0.768 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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 |
|---|---|---|---|---|
CRCB | PF02537.22 | 3.1e-28 | 11–120 | CrcB-like protein, Camphor Resistance (CrcB) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: crcB (fluoride ion transporter CrcB), high confidence from genomic context alone (score 986 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3070 crcB |
fluoride ion transporter CrcB | 989 | 986 ctx | neighborhood:882 cooccurence:773 coexpression:524 |
Rv3071 hyp |
hypothetical protein | 936 | 926 ctx | neighborhood:881 cooccurence:402 |
Rv3068c pgmA |
phosphoglucomutase PgmA | 787 | 787 ctx | neighborhood:785 |
Rv1022 lpqU |
lipoprotein LpqU | 886 | 165 | textmining:870 |
Rv1280c oppA |
oligopeptide ABC transporter substrate-binding lipoprotein OppA | 569 | 155 | textmining:511 |
Rv0418 lpqL |
lipoprotein aminopeptidase LpqL | 656 | 49 | textmining:654 |
Rv0361 |
membrane protein | 870 | 47 | textmining:870 |
Rv1733c |
transmembrane protein | 513 | 47 | textmining:510 |
Rv0200 |
transmembrane protein | 752 | 46 | textmining:751 |
Rv0556 |
transmembrane protein | 870 | 44 | textmining:870 |
Rv3630 |
integral membrane protein | 861 | 44 | textmining:861 |
Rv0835 lpqQ |
lipoprotein LpqQ | 860 | 41 | textmining:860 |
Rv0403c mmpS1 |
membrane protein MmpS1 | 753 | 41 | textmining:753 |
Rv0178 |
Mce associated membrane protein | 629 | 41 | textmining:629 |
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: fluoride ion transporter CrcB
- MTBC0 PGAP product: fluoride efflux transporter CrcB
- Pfam (hmmscan --cut_ga): CRCB PF02537.22 (E=3e-28)
- (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_217585.1)
- Domains: Pfam-A via hmmscan --cut_ga — CRCB (PF02537.22)
- 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
COG0239 - Curated reference: UniProt P9WP63 (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 —
14 functional partner(s); context anchor
crcB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003262|Rv3069|crcB MPNHDYRELAAVFAGGALGALARAALSALAIPDPARWPWPTFTVNVVGAFLVGYFTTRLLERLPLSSYRRPLLGTGLCGGLTTFSTMQVETISMIEHGHWGLAAAYSVVSITLGLLAVHLATVLVRRVRIRR