fadE27 Family assigned · medium auto-curated
H37Rv Rv3505 · MTBC0 mtbc0_003720 ·
373 aa · 3948280–3949401 (+) ·
RefSeq NP_218022.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acyl-CoA dehydrogenase FadE27 |
|---|---|
| MTBC0 PGAP re-annotation | acyl-CoA dehydrogenase family protein |
| Revised (this work) | Acyl-CoA dehydrogenase family protein. Pfam: Acyl-CoA_dh_N (PF02771.22), Acyl-CoA_dh_1 (PF00441.30), Acyl-CoA_dh_2 (PF08028.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y3Q0
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Acyl-CoA dehydrogenase FadE27 |
| EC (curated) |
EC 1.3.99.-
|
| Curated function | Involved in the first cycle of side chain dehydrogenation in the beta-oxidation of cholesterol catabolism. It contributes partly to the virulence by increasing the efficiency of beta-oxidation. Catalyzes the dehydrogenation of acyl-CoA ester side chains of (25S)-3-oxo-cholest-4-en-26-oyl-CoA (3-OCS-CoA) to yield (24E)-3-oxo-cholest-4,24-dien-26-oyl-CoA. Also able to dehydrogenate steroyl-CoA such as 3-oxo-chol-4-en-24-oyl-CoA (3-OCO-CoA) as well as 3-oxo-4-pregnene-20-carboxyl-CoA (3-OPC-CoA). It dehydrogenates only (25S)-OCS-CoA diastereomer. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | fadE27 |
| eggNOG description | acyl-CoA dehydrogenase |
| Orthologous group | COG1960 |
| EC number |
EC 1.3.8.7
|
| KEGG orthology |
K00249
|
| KEGG pathways |
map00071, map00280, map00410, map00640, map01100, map01110, map01130, map01200, map01212, map03320
|
| KEGG modules |
M00013, M00036, M00087
|
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 | 0.295 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 4 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.54% of strains (780) · clonal |
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 |
|---|---|---|---|---|
Acyl-CoA_dh_N | PF02771.22 | 2.5e-12 | 7–117 | Acyl-CoA dehydrogenase, N-terminal domain |
Acyl-CoA_dh_1 | PF00441.30 | 1.8e-23 | 223–368 | Acyl-CoA dehydrogenase, C-terminal domain |
Acyl-CoA_dh_2 | PF08028.17 | 2.6e-10 | 231–344 | Acyl-CoA dehydrogenase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadE26 (acyl-CoA dehydrogenase FadE26), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3504 fadE26 |
acyl-CoA dehydrogenase FadE26 | 999 | 1000 ctx | neighborhood:846 cooccurence:773 coexpression:458 experimental:999 database:900 textmining:946 |
Rv3502c |
3-oxoacyl-ACP reductase | 860 | 843 ctx | neighborhood:717 |
Rv3516 echA19 |
enoyl-CoA hydratase EchA19 | 876 | 819 | database:643 |
Rv3028c fixB |
electron transfer flavoprotein subunit alpha | 816 | 809 ctx | cooccurence:472 coexpression:410 experimental:419 |
Rv3506 fadD17 |
long-chain-fatty-acid--CoA ligase FadD17 | 917 | 808 ctx | neighborhood:792 textmining:586 |
Rv3543c fadE29 |
acyl-CoA dehydrogenase FadE29 | 857 | 799 ctx | cooccurence:772 |
Rv3029c fixA |
electron transfer flavoprotein subunit beta | 806 | 798 ctx | cooccurence:450 coexpression:404 experimental:418 |
Rv0860 fadB |
fatty oxidation protein FadB | 803 | 788 | coexpression:647 |
Rv3562 fadE31 |
acyl-CoA dehydrogenase FadE31 | 906 | 760 ctx | cooccurence:759 textmining:627 |
Rv3560c fadE30 |
acyl-CoA dehydrogenase FadE30 | 795 | 751 ctx | cooccurence:751 |
Rv1934c fadE17 |
acyl-CoA dehydrogenase FadE17 | 808 | 739 ctx | cooccurence:738 |
Rv3541c chsH1 hyp |
hypothetical protein | 747 | 738 ctx | cooccurence:502 |
Rv1679 fadE16 |
acyl-CoA dehydrogenase FadE16 | 737 | 737 ctx | cooccurence:737 |
Rv0752c fadE9 |
acyl-CoA dehydrogenase FadE9 | 737 | 737 ctx | cooccurence:735 |
Rv3550 echA20 |
enoyl-CoA hydratase EchA20 | 810 | 701 |
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: acyl-CoA dehydrogenase FadE27
- MTBC0 PGAP product: acyl-CoA dehydrogenase family protein
- Pfam (hmmscan --cut_ga): Acyl-CoA_dh_N PF02771.22 (E=2e-12), Acyl-CoA_dh_1 PF00441.30 (E=2e-23), Acyl-CoA_dh_2 PF08028.17 (E=3e-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_218022.1)
- Domains: Pfam-A via hmmscan --cut_ga — Acyl-CoA_dh_N (PF02771.22), Acyl-CoA_dh_1 (PF00441.30), Acyl-CoA_dh_2 (PF08028.17)
- 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
COG1960 - Curated reference: UniProt I6Y3Q0 (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 —
138 functional partner(s); context anchor
fadE26 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003720|Rv3505|fadE27 MDFTTTEAAQDLGGLVDTIVDAVCTPEHQRELDKLEQRFDRELWRKLIDAGILSSAAPESLGGDGFGVLEQVAVLVALGHQLAAVPYLESVVLAAGALARFGSPELQQGWGVSAVSGDRILTVALDGEMGEGPVQAAGTGHGYRLTGTRTQVGYGPVADAFLVPAETDSGAAVFLVAAGDPGVAVTALATTGLGSVGHLELNGAKVDAARRVGGTDVAVWLGTLSTLSRTAFQLGVLERGLQMTAEYARTREQFDRPIGSFQAVGQRLADGYIDVKGLRLTLTQAAWRVAEDSLASRECPQPADIDVATAGFWAAEAGHRVAHTIVHVHGGVGVDTDHPVHRYFLAAKQTEFALGGATGQLRRIGRELAETPA