Rv3502c Resolved · high auto-curated
H37Rv Rv3502c · MTBC0 mtbc0_003717 ·
317 aa · 3945669–3946622 (-) ·
RefSeq NP_218019.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 3-oxoacyl-ACP reductase |
|---|---|
| MTBC0 PGAP re-annotation | 3-oxoacyl-ACP reductase |
| Revised (this work) | 3-oxoacyl-ACP reductase. 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 |
O53547
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Hydroxyacyl-CoA dehydrogenase ChsB1 |
| EC (curated) |
EC 1.1.1.-
|
| Curated function | A reversible dehydrogenase involved in cholesterol side-chain degradation. Catalyzes the oxidation of hydroxyl-cholesterol-CoA ester metabolic intermediate (22S)-HOCO-CoA (3-oxo-chol-4-ene-(22S)-hydroxy-24-oyl-CoA), the product of ChsH3, has no activity on (22R)-HOCO-CoA (the product of EchA19). Also acts on (3R)-hydroxyoctanoyl-CoA and 17-beta-hydroxyandrost-4-en-3-one, but not on 7-alpha-hydroxyandrost-4-en-3-one, uses NAD(+) but not NADP(+). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | hsd4A |
| eggNOG description | Belongs to the short-chain dehydrogenases reductases (SDR) family |
| Orthologous group | COG1028 |
| EC number |
EC 1.1.1.100
|
| KEGG orthology |
K00059
|
| KEGG pathways |
map00061, map00333, map00780, map01040, map01100, map01130, map01212
|
| KEGG modules |
M00083, M00572
|
| Gene Ontology (62) |
GO:0003674, GO:0003824, GO:0004303, GO:0005488, GO:0005515, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005777, GO:0006066, GO:0006629 +50 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 | 0.369 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 3 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 | 1.1e-38 | 21–219 | short chain dehydrogenase |
KR | PF08659.17 | 6.3e-15 | 24–194 | KR domain |
adh_short_C2 | PF13561.13 | 2.5e-31 | 27–263 | Enoyl-(Acyl carrier protein) reductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3538 (dehydrogenase), high confidence from genomic context alone (score 956 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3538 |
dehydrogenase | 955 | 956 ctx | fusion:900 |
Rv3389c htdY |
3-hydroxyacyl-thioester dehydratase HtdY | 947 | 947 ctx | fusion:900 |
Rv3504 fadE26 |
acyl-CoA dehydrogenase FadE26 | 938 | 872 ctx | neighborhood:736 textmining:541 |
Rv3505 fadE27 |
acyl-CoA dehydrogenase FadE27 | 860 | 843 ctx | neighborhood:717 |
Rv2524c fas |
fatty acid synthase | 826 | 800 | coexpression:506 experimental:475 |
Rv3549c |
short-chain type dehydrogenase/reductase | 774 | 774 ctx | cooccurence:773 |
Rv3530c |
oxidoreductase | 768 | 769 ctx | cooccurence:766 |
Rv3506 fadD17 |
long-chain-fatty-acid--CoA ligase FadD17 | 784 | 753 ctx | neighborhood:676 |
Rv3485c |
short-chain type dehydrogenase/reductase | 751 | 751 ctx | cooccurence:751 |
Rv3503c fdxD |
ferredoxin FdxD | 726 | 726 ctx | neighborhood:717 |
Rv1050 |
oxidoreductase | 709 | 709 ctx | cooccurence:702 |
Rv3492c |
Mce associated protein | 701 | 700 ctx | neighborhood:520 |
Rv3541c chsH1 hyp |
hypothetical protein | 701 | 665 ctx | cooccurence:512 |
Rv0765c |
oxidoreductase | 645 | 646 ctx | cooccurence:633 |
Rv3562 fadE31 |
acyl-CoA dehydrogenase FadE31 | 663 | 622 ctx | cooccurence: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: 3-oxoacyl-ACP reductase
- MTBC0 PGAP product: 3-oxoacyl-ACP reductase
- Pfam (hmmscan --cut_ga): adh_short PF00106.32 (E=1e-38), KR PF08659.17 (E=6e-15), adh_short_C2 PF13561.13 (E=3e-31)
- (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_218019.1)
- 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 O53547 (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 —
121 functional partner(s); context anchor
Rv3538 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003717|Rv3502c| MKLTESNRSPRTTNTTDLSGKVAVVTGAAAGLGRAEALGLARLGATVVVNDVASALDASDVVDEIGAAAADAGAKAVAVAGDISQRATADELLASAVGLGGLDIVVNNAGITRDRMLFNMSDEEWDAVIAVHLRGHFLLTRNAAAYWRDKAKDAEGGSVFGRLVNTSSEAGLVGPVGQANYAAAKAGITALTLSAARALGRYGVCANVICPRARTAMTADVFGAAPDVEAGQIDPLSPQHVVSLVQFLASPAAAEVNGQVFIVYGPQVTLVSPPHMERRFSADGTSWDPTELTATLRDYFAGRDPEQSFSATDLMRQ