fadE28 Resolved · high auto-curated
H37Rv Rv3544c · MTBC0 mtbc0_003761 ·
339 aa · 4006802–4007821 (-) ·
RefSeq NP_218061.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acyl-CoA dehydrogenase FadE28 |
|---|---|
| MTBC0 PGAP re-annotation | acyl-CoA dehydrogenase FadE28 |
| Revised (this work) | Acyl-CoA dehydrogenase FadE28. Pfam: Acyl-CoA_dh_N (PF02771.22), Acyl-CoA_dh_1 (PF00441.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71857
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Acyl-CoA dehydrogenase FadE28 |
| EC (curated) |
EC 1.3.99.-
|
| Curated function | Involved in the third cycle of side chain dehydrogenation in the beta-oxidation of cholesterol catabolism. May play an important role for the initial macrophage invasion, possibly in response to the acidification of phagosome. It contributes partly to the virulence by increasing the efficiency of beta-oxidation. Catalyzes the dehydrogenation of 2'-propanoyl-CoA ester side chains of 3-oxo-4-pregnene-20-carboxyl-CoA (3-OPC-CoA) to yield 3-oxo-4,17-pregnadiene-20-carboxyl-CoA (3-OPDC-CoA). Also able to dehydrogenate steroyl-CoA such as 3-oxo-chol-4-en-24-oyl-CoA (3-OCO-CoA), 1beta-(2'-propanoyl-C. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | fadE28 |
| eggNOG description | acyl-CoA dehydrogenase |
| Orthologous group | COG1960 |
| Gene Ontology (67) |
GO:0000166, GO:0003674, GO:0005488, GO:0006066, GO:0006082, GO:0006629, GO:0006631, GO:0006635, GO:0006706, GO:0006707, GO:0008150, GO:0008152 +55 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 | 0.246 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 2 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 |
|---|---|---|---|---|
Acyl-CoA_dh_N | PF02771.22 | 7.6e-09 | 20–99 | Acyl-CoA dehydrogenase, N-terminal domain |
Acyl-CoA_dh_1 | PF00441.30 | 2.1e-15 | 204–327 | Acyl-CoA dehydrogenase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadE29 (acyl-CoA dehydrogenase FadE29), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3543c fadE29 |
acyl-CoA dehydrogenase FadE29 | 999 | 1000 ctx | neighborhood:882 fusion:480 cooccurence:773 coexpression:730 database:900 textmining:979 |
Rv3541c chsH1 hyp |
hypothetical protein | 997 | 989 ctx | neighborhood:881 cooccurence:674 database:639 textmining:810 |
Rv3542c chsH2 hyp |
hypothetical protein | 980 | 980 ctx | neighborhood:881 cooccurence:674 database:500 |
Rv3540c ltp2 |
lipid transfer protein | 995 | 962 ctx | neighborhood:881 cooccurence:476 textmining:878 |
Rv3546 fadA5 |
acetyl-CoA acetyltransferase FadA | 988 | 942 ctx | neighborhood:778 database:500 textmining:815 |
Rv3545c cyp125 |
steroid C26-monooxygenase | 987 | 929 ctx | neighborhood:882 textmining:833 |
Rv3504 fadE26 |
acyl-CoA dehydrogenase FadE26 | 915 | 823 ctx | cooccurence:773 textmining:542 |
Rv3522 ltp4 |
lipid transfer protein | 897 | 789 ctx | cooccurence:642 textmining:535 |
Rv0860 fadB |
fatty oxidation protein FadB | 809 | 788 | coexpression:647 |
Rv3563 fadE32 |
acyl-CoA dehydrogenase FadE32 | 920 | 769 ctx | cooccurence:768 textmining:668 |
Rv3028c fixB |
electron transfer flavoprotein subunit alpha | 776 | 767 | coexpression:408 experimental:419 |
Rv3562 fadE31 |
acyl-CoA dehydrogenase FadE31 | 761 | 761 ctx | cooccurence:760 |
Rv3029c fixA |
electron transfer flavoprotein subunit beta | 769 | 760 | coexpression:404 experimental:418 |
Rv3560c fadE30 |
acyl-CoA dehydrogenase FadE30 | 890 | 758 ctx | cooccurence:757 textmining:566 |
Rv3550 echA20 |
enoyl-CoA hydratase EchA20 | 868 | 737 ctx | cooccurence:408 textmining:520 |
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 FadE28
- MTBC0 PGAP product: acyl-CoA dehydrogenase FadE28
- Pfam (hmmscan --cut_ga): Acyl-CoA_dh_N PF02771.22 (E=8e-09), Acyl-CoA_dh_1 PF00441.30 (E=2e-15)
- (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_218061.1)
- Domains: Pfam-A via hmmscan --cut_ga — Acyl-CoA_dh_N (PF02771.22), Acyl-CoA_dh_1 (PF00441.30)
- 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 P71857 (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 —
156 functional partner(s); context anchor
fadE29 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003761|Rv3544c|fadE28 MDFDPTAEQQAVADVVTSVLERDISWEALVCGGVTALPVPERLGGDGVGLFEVGALLTEVGRHGAVTPALATLGLGVVPLLELASAEQQDRFLAGVAKGGVLTAALNEPGAALPDRPATSFVGGRLSGTKVGVGYAEQADWMLVTADNAVVVVSPTADGVRMVRTPTSNGSDEYVMTMDGVAVADCDILADVAAHRVNQLALAVMGAYADGLVAGALRLTADYVANRKQFGKPLSTFQTVAAQLAEVYIASRTIDLVAKSVIWRLAEDLDAGDDLGVLGYWVTSQAPPAMQICHHLHGGMGMDVTYPMHRYYSTIKDLTRLLGGPSHRLELLGARCSLT