Rv2054 Family assigned · medium auto-curated
H37Rv Rv2054 · MTBC0 mtbc0_002187 ·
237 aa · 2341738–2342451 (+) ·
RefSeq NP_216570.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | dienelactone hydrolase family protein |
| Revised (this work) | Dienelactone hydrolase family protein. Pfam: DLH (PF01738.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O86353
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | dienelactone hydrolase |
| Orthologous group | COG0412 |
| EC number |
EC 3.1.1.45
|
| KEGG orthology |
K01061
|
| KEGG pathways |
map00361, map00364, map00623, map01100, map01110, map01120, map01130
|
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, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.11% of strains (157) · 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 |
|---|---|---|---|---|
DLH | PF01738.25 | 9.5e-64 | 13–228 | Dienelactone hydrolase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fxsA (transmembrane protein FxsA), high confidence from genomic context alone (score 787 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) |
|---|---|---|---|---|
Rv2765 |
hydrolase | 925 | 926 | database:900 |
Rv2053c fxsA |
transmembrane protein FxsA | 787 | 787 ctx | neighborhood:784 |
Rv2052c hyp |
hypothetical protein | 671 | 671 ctx | neighborhood:671 |
Rv1832 gcvB |
glycine dehydrogenase | 441 | 441 | coexpression:422 |
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: dienelactone hydrolase family protein
- Pfam (hmmscan --cut_ga): DLH PF01738.25 (E=1e-63)
- (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_216570.1)
- Domains: Pfam-A via hmmscan --cut_ga — DLH (PF01738.25)
- 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
COG0412 - Curated reference: UniProt O86353 (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 —
4 functional partner(s); context anchor
fxsA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002187|Rv2054| MTTIEIDAPAGPIDALLGLPPGQGPWPGVVVVHDAVGYVPDNKLISERIARAGYVVLTPNMYARGGRARCITRVFRELLTKRGRALDDILAARDHLLAMPECSGRVGIVGFCMGGQFALVLSPRGFGATAPFYGTPLPRHLSETLNGACPIVASFGTRDPLGIGAANRLRKVTAAKNIPADIKSYPGAGHSFANKLPGQPLVRIAGFGYNEAATEDAWRRVFEFFGQHLRAGSPGEP