Rv3485c Resolved · high auto-curated
H37Rv Rv3485c · MTBC0 - ·
314 aa · 3904622–3905566 (-) ·
RefSeq NP_218002.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | short-chain type dehydrogenase/reductase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Short-chain type dehydrogenase/reductase. Pfam: SDR (PF23441.1), KR (PF08659.17), adh_short (PF00106.32), Epimerase (PF01370.28), 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.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O06348
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable short-chain type dehydrogenase/reductase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | Dehydrogenase |
| Orthologous group | COG1028 |
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 | 0.348 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 4 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 |
|---|---|---|---|---|
SDR | PF23441.1 | 5.2e-07 | 45–290 | SDR-like rossmann domain |
KR | PF08659.17 | 5.5e-17 | 47–209 | KR domain |
adh_short | PF00106.32 | 1.5e-44 | 48–239 | short chain dehydrogenase |
Epimerase | PF01370.28 | 7.3e-05 | 49–215 | NAD dependent epimerase/dehydratase family |
adh_short_C2 | PF13561.13 | 4.3e-58 | 55–287 | Enoyl-(Acyl carrier protein) reductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2129c (oxidoreductase), high confidence from genomic context alone (score 769 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2524c fas |
fatty acid synthase | 828 | 802 | coexpression:511 experimental:475 |
Rv2129c |
oxidoreductase | 769 | 769 ctx | cooccurence:762 |
Rv3502c |
3-oxoacyl-ACP reductase | 751 | 751 ctx | cooccurence:751 |
Rv0547c |
oxidoreductase | 704 | 693 ctx | cooccurence:651 |
Rv1882c |
short-chain type dehydrogenase/reductase | 689 | 690 ctx | cooccurence:673 |
Rv3548c |
short-chain type dehydrogenase/reductase | 682 | 682 ctx | cooccurence:679 |
Rv0945 |
oxidoreductase | 677 | 666 ctx | cooccurence:618 |
Rv0148 |
short-chain type dehydrogenase/reductase | 590 | 590 ctx | cooccurence:589 |
Rv0073 |
glutamine ABC transporter ATP-binding protein | 605 | 587 | database:431 |
Rv2564 glnQ |
glutamine ABC transporter ATP-binding protein | 601 | 583 | database:431 |
Rv3486 hyp |
hypothetical protein | 554 | 554 ctx | neighborhood:490 |
Rv1937 |
oxygenase | 593 | 545 | |
Rv3728 |
membrane protein | 556 | 532 | database:431 |
Rv2299c htpG |
chaperone protein HtpG | 539 | 520 | database:450 |
Rv0125 pepA |
serine protease PepA | 528 | 517 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): short-chain type dehydrogenase/reductase
- Pfam (hmmscan --cut_ga): SDR PF23441.1 (E=5e-07), KR PF08659.17 (E=6e-17), adh_short PF00106.32 (E=2e-44), Epimerase PF01370.28 (E=7e-05), adh_short_C2 PF13561.13 (E=4e-58)
- (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_218002.1)
- Domains: Pfam-A via hmmscan --cut_ga — SDR (PF23441.1), KR (PF08659.17), adh_short (PF00106.32), Epimerase (PF01370.28), 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 O06348 (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 —
84 functional partner(s); context anchor
Rv2129c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3485c| MNSRAPRNLAVSSPSAQVTGRMVQNGENLFQFRREGPQVQLSFQDRTYLVTGGGSGIGKGVAAGLVAAGAAVMIVGRNPDKLAAAVKDIEALKTGAIGYEPADITDEEQTLRVVDAATAWHGRLHGVVHCAGGSQTIGPITQIDSQAWRRTVDLNVNGTMYVLKHAARELVRGGGGSFVGISSIAASNTHRWFGAYGVTKSAVDHMMKLAADELGPSWVRVNSIRPGLIRTDLVVPVTESPELSADYRVCTPLPRVGEVEDVANLAMFLLSDAASWITGQVINVDGGHMLRRGPDFSPMLEPVFGADGLRGVVG