fadE29 Resolved · high auto-curated
H37Rv Rv3543c · MTBC0 mtbc0_003760 ·
387 aa · 4005654–4006817 (-) ·
RefSeq NP_218060.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acyl-CoA dehydrogenase FadE29 |
|---|---|
| MTBC0 PGAP re-annotation | acyl-CoA dehydrogenase FadE29 |
| Revised (this work) | Acyl-CoA dehydrogenase FadE29. Pfam: Acyl-CoA_dh_N (PF02771.22), Acyl-CoA_dh_M (PF02770.25), 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 |
P71858
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Acyl-CoA dehydrogenase FadE29 |
| EC (curated) |
EC 1.3.99.-
|
| Curated function | Involved in the third cycle of side chain dehydrogenation in the beta-oxidation of cholesterol catabolism. 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-CoA)-3a-alpha-H- 7a-beta-methylhexahydro-4-indanone (indanone-CoA ester), hexahydroindanone and pregenenone. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | fadE29 |
| eggNOG description | acyl-CoA dehydrogenase |
| Orthologous group | COG1960 |
| Gene Ontology (63) |
GO:0000166, GO:0003674, GO:0005488, GO:0006066, GO:0006082, GO:0006629, GO:0006631, GO:0006635, GO:0006706, GO:0006707, GO:0008150, GO:0008152 +51 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 | 0.54 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
Acyl-CoA_dh_N | PF02771.22 | 4.5e-21 | 6–118 | Acyl-CoA dehydrogenase, N-terminal domain |
Acyl-CoA_dh_M | PF02770.25 | 4.6e-20 | 122–207 | Acyl-CoA dehydrogenase, middle domain |
Acyl-CoA_dh_1 | PF00441.30 | 2.1e-25 | 228–378 | Acyl-CoA dehydrogenase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadE28 (acyl-CoA dehydrogenase FadE28), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3544c fadE28 |
acyl-CoA dehydrogenase FadE28 | 999 | 1000 ctx | neighborhood:882 fusion:480 cooccurence:773 coexpression:730 database:900 textmining:979 |
Rv3541c chsH1 hyp |
hypothetical protein | 999 | 994 ctx | neighborhood:881 cooccurence:757 database:639 textmining:857 |
Rv3542c chsH2 hyp |
hypothetical protein | 994 | 990 ctx | neighborhood:881 cooccurence:747 coexpression:421 database:500 textmining:478 |
Rv3540c ltp2 |
lipid transfer protein | 998 | 980 ctx | neighborhood:881 cooccurence:602 coexpression:577 textmining:907 |
Rv3546 fadA5 |
acetyl-CoA acetyltransferase FadA | 995 | 944 ctx | neighborhood:778 database:500 textmining:919 |
Rv3545c cyp125 |
steroid C26-monooxygenase | 983 | 916 ctx | neighborhood:882 textmining:816 |
Rv3522 ltp4 |
lipid transfer protein | 968 | 838 ctx | cooccurence:721 textmining:815 |
Rv3505 fadE27 |
acyl-CoA dehydrogenase FadE27 | 857 | 799 ctx | cooccurence:772 |
Rv3550 echA20 |
enoyl-CoA hydratase EchA20 | 931 | 796 ctx | cooccurence:537 textmining:680 |
Rv0860 fadB |
fatty oxidation protein FadB | 828 | 788 | coexpression:647 |
Rv3523 ltp3 |
lipid carrier protein | 963 | 781 ctx | cooccurence:624 textmining:840 |
Rv3564 fadE33 |
acyl-CoA dehydrogenase FadE33 | 922 | 779 ctx | cooccurence:760 textmining:662 |
Rv3563 fadE32 |
acyl-CoA dehydrogenase FadE32 | 929 | 774 ctx | cooccurence:771 textmining:702 |
Rv1933c fadE18 |
acyl-CoA dehydrogenase FadE18 | 769 | 770 ctx | cooccurence:727 |
Rv3521 hyp |
hypothetical protein | 793 | 753 ctx | cooccurence:745 |
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 FadE29
- MTBC0 PGAP product: acyl-CoA dehydrogenase FadE29
- Pfam (hmmscan --cut_ga): Acyl-CoA_dh_N PF02771.22 (E=4e-21), Acyl-CoA_dh_M PF02770.25 (E=5e-20), Acyl-CoA_dh_1 PF00441.30 (E=2e-25)
- (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_218060.1)
- Domains: Pfam-A via hmmscan --cut_ga — Acyl-CoA_dh_N (PF02771.22), Acyl-CoA_dh_M (PF02770.25), 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 P71858 (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 —
144 functional partner(s); context anchor
fadE28 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003760|Rv3543c|fadE29 MFIDLTPEQRQLQAEIRQYFSNLISPDERTEMEKDRHGPAYRAVIRRMGRDGRLGVGWPKEFGGLGFGPIEQQIFVNEAHRADVPLPAVTLQTVGPTLQAHGSELQKKKFLPAILAGEAHFAIGYTEPEAGTDLASLRTTAVRDGDHYIVNGQKVFTTGAHDADYIWLACRTDPNAAKHKGISILIVDTKDPGYSWTPIILADGAHHTNATYYNDVRVPVDMLVGKENDGWRLITTQLNNERVMLGPAGRFASIYDRVHAWASVPGGNGVTPIDHDDVKRALGEIRAIWRINELLNWQVASAGEDINMADAAATKVFGTERVQRAGRLAEEIVGKYGNPAEPDTAELLRWLDAQTKRNLVITFGGGVNEVMREMIAASGLKVPRVPR