Rv3292 Family assigned · medium auto-curated
H37Rv Rv3292 · MTBC0 mtbc0_003500 ·
415 aa · 3694408–3695655 (+) ·
RefSeq NP_217809.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | VOC family protein |
| Revised (this work) | VOC family protein. Pfam: HGLS (PF07063.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WL01
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 2-oxoadipate dioxygenase/decarboxylase |
| EC (curated) |
EC 1.13.11.93
|
| Curated function | Catalyzes the decarboxylation and hydroxylation of 2-oxoadipate (2OA) to form D-2-hydroxyglutarate (D-2-HGA). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | DUF1338 |
| Orthologous group | COG5383 |
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 | 0.179 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
HGLS | PF07063.20 | 2.8e-121 | 16–370 | 2-oxoadipate dioxygenase/decarboxylase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pcd (piperideine-6-carboxylic acid dehydrogenase), high confidence from genomic context alone (score 979 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) |
|---|---|---|---|---|
Rv3293 pcd |
piperideine-6-carboxylic acid dehydrogenase | 978 | 979 ctx | neighborhood:843 coexpression:799 |
Rv3291c lrpA |
transcriptional regulator LrpA | 840 | 841 ctx | neighborhood:790 |
Rv3290c lat |
L-lysine-epsilon aminotransferase | 648 | 635 ctx | neighborhood:526 |
Rv3289c |
transmembrane protein | 539 | 539 ctx | neighborhood:516 |
Rv3288c usfY hyp |
hypothetical protein | 437 | 437 ctx | neighborhood:406 |
Rv2476c gdh |
NAD-dependent glutamate dehydrogenase | 412 | 412 | coexpression:412 |
Rv3295 |
TetR family transcriptional regulator | 403 | 403 |
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: VOC family protein
- Pfam (hmmscan --cut_ga): HGLS PF07063.20 (E=3e-121)
- (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_217809.1)
- Domains: Pfam-A via hmmscan --cut_ga — HGLS (PF07063.20)
- 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
COG5383 - Curated reference: UniProt P9WL01 (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 —
7 functional partner(s); context anchor
pcd - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003500|Rv3292| MSRSKRLQTGQLRARFAAGLSAMYAAEVPAYGTLVEVCAQVNSDYLTRHRRAERLGSLQRVTAERHGAIRVGNPAELAAVADLFAAFGMLPVGYYDLRTAESPIPVVSTAFRPIDANELAHNPFRVFTSMLAIEDRRYFDADLRTRVQTFLARRQLFDPALLAQARAIAADGGCDADDAPAFVAAAVAAFALSREPVEKSWYDELSRVSAVAADIAGVGSTHINHLTPRVLDIDDLYRRMTERGITMIDTIQGPPRTDGPDVLLRQTSFRALAEPRMFRDEDGTVTPGILRVRFGEVEARGVALTPRGRERYEAAMAAADPAAVWATHFPSTDAEMAAQGLAYYRGGDPSAPIVYEDFLPASAAGIFRSNLDRDSQTGDGPDDAGYNVDWLAGAIGRHIHDPYALYDALAQEERR