Rv0148 Family assigned · medium auto-curated
H37Rv Rv0148 · MTBC0 mtbc0_000159 ·
286 aa · 175179–176039 (+) ·
RefSeq NP_214662.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | short-chain type dehydrogenase/reductase |
|---|---|
| MTBC0 PGAP re-annotation | SDR family oxidoreductase |
| Revised (this work) | SDR family oxidoreductase. Pfam: adh_short (PF00106.32), KR (PF08659.17), adh_short_C2 (PF13561.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96825
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative short-chain type dehydrogenase/reductase Rv0148 |
| EC (curated) |
EC 1.1.1.-
|
UniProt still lists this protein as Putative short-chain type dehydrogenase/reductase Rv0148; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | Belongs to the short-chain dehydrogenases reductases (SDR) family |
| Orthologous group | COG1028 |
| Gene Ontology (28) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006464, GO:0006807, GO:0008150, GO:0008152, GO:0009987, GO:0016020, GO:0018193, GO:0018205 +16 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 |
|---|---|---|---|---|
adh_short | PF00106.32 | 4.1e-38 | 7–204 | short chain dehydrogenase |
KR | PF08659.17 | 9.0e-22 | 9–177 | KR domain |
adh_short_C2 | PF13561.13 | 2.6e-28 | 13–217 | Enoyl-(Acyl carrier protein) reductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: htdY (3-hydroxyacyl-thioester dehydratase HtdY), high confidence from genomic context alone (score 970 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3389c htdY |
3-hydroxyacyl-thioester dehydratase HtdY | 970 | 970 ctx | fusion:900 cooccurence:583 |
Rv3538 |
dehydrogenase | 956 | 956 ctx | fusion:900 |
Rv0149 |
quinone oxidoreductase | 903 | 903 ctx | neighborhood:882 |
Rv0242c fabG4 |
3-oxoacyl-ACP reductase FabG | 899 | 899 ctx | fusion:899 |
Rv0147 |
aldehyde dehydrogenase | 889 | 885 ctx | neighborhood:789 |
Rv2524c fas |
fatty acid synthase | 828 | 803 | coexpression:512 experimental:475 |
Rv0146 |
S-adenosylmethionine-dependent methyltransferase | 708 | 708 ctx | neighborhood:699 |
Rv0145 |
S-adenosylmethionine-dependent methyltransferase | 641 | 642 ctx | neighborhood:625 |
Rv3485c |
short-chain type dehydrogenase/reductase | 590 | 590 ctx | cooccurence:589 |
Rv0998 |
acetyltransferase Pat | 585 | 584 | database:431 |
Rv2246 kasB |
3-oxoacyl-ACP synthase 2 | 591 | 567 | |
Rv0130 htdZ |
3-hydroxyl-thioester dehydratase | 583 | 565 | |
Rv2565 |
NTE family protein | 578 | 561 | database:431 |
Rv2766c |
short-chain type dehydrogenase/reductase | 607 | 558 ctx | cooccurence:557 |
Rv2245 kasA |
3-oxoacyl-ACP synthase 1 | 581 | 557 |
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: short-chain type dehydrogenase/reductase
- MTBC0 PGAP product: SDR family oxidoreductase
- Pfam (hmmscan --cut_ga): adh_short PF00106.32 (E=4e-38), KR PF08659.17 (E=9e-22), adh_short_C2 PF13561.13 (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_214662.1)
- Domains: Pfam-A via hmmscan --cut_ga — adh_short (PF00106.32), KR (PF08659.17), adh_short_C2 (PF13561.13)
- 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
COG1028 - Curated reference: UniProt P96825 (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 —
97 functional partner(s); context anchor
htdY - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000159|Rv0148| MPGVQDRVIVVTGAGGGLGREYALTLAGEGASVVVNDLGGARDGTGAGSAMADEVVAEIRDKGGRAVANYDSVATEDGAANIIKTALDEFGAVHGVVSNAGILRDGTFHKMSFENWDAVLKVHLYGGYHVLRAAWPHFREQSYGRVVVATSTSGLFGNFGQTNYGAAKLGLVGLINTLALEGAKYNIHANALAPIAATRMTQDILPPEVLEKLTPEFVAPVVAYLCTEECADNASVYVVGGGKVQRVALFGNDGANFDKPPSVQDVAARWAEITDLSGAKIAGFKL