Rv0143c Resolved · high auto-curated
H37Rv Rv0143c · MTBC0 mtbc0_000154 ·
492 aa · 169050–170528 (-) ·
RefSeq NP_214657.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | chloride channel protein |
| Revised (this work) | Chloride channel protein. Pfam: Voltage_CLC (PF00654.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96820
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | clcA |
| eggNOG description | Chloride channel |
| Orthologous group | COG0038 |
| KEGG orthology |
K03281
|
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 | 0.487 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 8 missense, 1 nonsense, 2 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 0.73% of strains (1056) · 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 |
|---|---|---|---|---|
Voltage_CLC | PF00654.26 | 3.0e-85 | 113–460 | Voltage gated chloride channel |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0144 (transcriptional regulator), medium confidence from genomic context alone (score 559 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0144 |
transcriptional regulator | 560 | 559 ctx | neighborhood:555 |
Rv1762c hyp |
hypothetical protein | 452 | 452 ctx | cooccurence:421 |
Rv2101 helZ |
helicase HelZ | 470 | 438 | |
Rv3432c gadB |
glutamate decarboxylase GadB | 466 | 432 | |
Rv0145 |
S-adenosylmethionine-dependent methyltransferase | 417 | 418 ctx | neighborhood:414 |
Rv0146 |
S-adenosylmethionine-dependent methyltransferase | 415 | 415 ctx | neighborhood:413 |
Rv3256c hyp |
hypothetical protein | 436 | 409 | coexpression:409 |
Rv1899c lppD |
lipoprotein LppD | 403 | 403 | |
Rv3907c pcnA |
poly(A) polymerase PcnA | 414 | 47 | textmining:411 |
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: transmembrane protein
- MTBC0 PGAP product: chloride channel protein
- Pfam (hmmscan --cut_ga): Voltage_CLC PF00654.26 (E=3e-85)
- (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_214657.1)
- Domains: Pfam-A via hmmscan --cut_ga — Voltage_CLC (PF00654.26)
- 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
COG0038 - Curated reference: UniProt P96820 (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 —
9 functional partner(s); context anchor
Rv0144 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000154|Rv0143c| MAPGDWSVFAWHAANLPTMPEAEDIGNEAAGGRFGVSIRSAGYLRKWFLLGITIGVIAGLGAVVFYLALKYTSEFLLGYLADYQIPTPVGEGGHRGSTGFARPWAIPLVTTGGAVLSALIVAKLAPEATGHGTDEAIESVHGDPRAIRGRAVLVKMVASALTIGSGGSGGREGPTAQISAGFCSLLTRRLNLSNEDGRTAVALGIGAGIGAIFAAPLGGAALGASIPYRDDFDYRNLLPGFIASGTAYAVLGAFLGFDPLFGYIDAEYRFEKAWPLLWFVVIGLIAAAVGYLYARVFHASVAITRRLPGGPVLKPAIGGLLVGLLGLPIPQILSSGYGWAQLAADRGTLLSIPLWIVIVLPIAKILATSLSIGTGGSGGLFGPGIVIGAFVGAAIWRLGELTELPGVPHEPGIFVVVAMMACFGSVSRAPLAVMIMVAEMTGSFSVVPGAIIAVGIAALLLSRTNVTIYETQRLNRQTAEAERGGSDRPTTA