Rv0484c Family assigned · medium auto-curated
H37Rv Rv0484c · MTBC0 mtbc0_000509 ·
251 aa · 576411–577166 (-) ·
RefSeq NP_214998.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | short-chain type oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | SDR family oxidoreductase |
| Revised (this work) | SDR family oxidoreductase. Pfam: adh_short (PF00106.32), KR (PF08659.17), Epimerase (PF01370.28), adh_short_C2 (PF13561.13), NAD_binding_10 (PF13460.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGR5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized oxidoreductase Rv0484c |
| EC (curated) |
EC 1.-.-.-
|
UniProt still lists this protein as Uncharacterized oxidoreductase Rv0484c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | sdh |
| eggNOG description | Belongs to the short-chain dehydrogenases reductases (SDR) family |
| Orthologous group | COG4221 |
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.378 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 5 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 | 2.5e-45 | 9–186 | short chain dehydrogenase |
KR | PF08659.17 | 5.6e-09 | 12–164 | KR domain |
Epimerase | PF01370.28 | 3.9e-08 | 12–120 | NAD dependent epimerase/dehydratase family |
adh_short_C2 | PF13561.13 | 7.0e-33 | 15–221 | Enoyl-(Acyl carrier protein) reductase |
NAD_binding_10 | PF13460.13 | 7.0e-10 | 15–140 | NAD(P)H-binding |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0485 (transcriptional regulator), high confidence from genomic context alone (score 775 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0485 |
transcriptional regulator | 775 | 775 ctx | neighborhood:763 |
Rv1832 gcvB |
glycine dehydrogenase | 684 | 684 ctx | fusion:681 |
Rv0489 gpm1 |
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | 620 | 621 ctx | neighborhood:618 |
Rv1714 |
oxidoreductase | 554 | 555 ctx | cooccurence:544 |
Rv1350 fabG2 |
3-oxoacyl-ACP reductase FabG | 552 | 552 ctx | cooccurence:543 |
Rv0487 hyp |
hypothetical protein | 480 | 480 ctx | neighborhood:479 |
Rv0486 mshA |
D-inositol 3-phosphate glycosyltransferase | 436 | 435 ctx | neighborhood:435 |
Rv0927c |
oxidoreductase | 419 | 420 ctx | cooccurence:407 |
Rv1932 tpx |
2-Cys peroxiredoxin | 409 | 410 | coexpression:410 |
Rv0490 senX3 |
two component sensor histidine kinase SenX3 | 404 | 404 | |
Rv0751c mmsB |
3-hydroxyisobutyrate dehydrogenase | 432 | 76 | textmining:411 |
Rv3205c hyp |
hypothetical protein | 872 | 63 | textmining:870 |
Rv0712 hyp |
hypothetical protein | 870 | 45 | textmining:870 |
Rv2837c nrnA |
bifunctional oligoribonuclease/PAP phosphatase NrnA | 870 | 44 | textmining:870 |
Rv1730c |
penicillin-binding protein | 753 | 43 | textmining:753 |
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 oxidoreductase
- MTBC0 PGAP product: SDR family oxidoreductase
- Pfam (hmmscan --cut_ga): adh_short PF00106.32 (E=2e-45), KR PF08659.17 (E=6e-09), Epimerase PF01370.28 (E=4e-08), adh_short_C2 PF13561.13 (E=7e-33), NAD_binding_10 PF13460.13 (E=7e-10)
- (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_214998.1)
- Domains: Pfam-A via hmmscan --cut_ga — adh_short (PF00106.32), KR (PF08659.17), Epimerase (PF01370.28), adh_short_C2 (PF13561.13), NAD_binding_10 (PF13460.13)
- 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
COG4221 - Curated reference: UniProt P9WGR5 (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 —
18 functional partner(s); context anchor
Rv0485 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000509|Rv0484c| MTTIGTRKRVAVVTGASSGIGEATARTLAAQGFHVVAVARRADRITALANQIGGTAIVADVTDDAAVEALARALSRVDVLVNNAGGAKGLQFVADADLEHWRWMWDTNVLGTLRVTRALLPKLIDSGDGLIVTVTSIAALEVYDGGAGYTAAKHAQGALHRTLRGELLGKPVRLTEIAPGAVETEFSLVRFDGDQQRADAVYAGMTPLVAADVAEVIGFVATRPSHVNLDQIVIRPRDQASASRRATHPVR