fadE25 Resolved · high auto-curated
H37Rv Rv3274c · MTBC0 mtbc0_003482 ·
389 aa · 3679063–3680232 (-) ·
RefSeq NP_217791.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acyl-CoA dehydrogenase |
|---|---|
| MTBC0 PGAP re-annotation | acyl-CoA dehydrogenase |
| Revised (this work) | Acyl-CoA dehydrogenase. Pfam: Acyl-CoA_dh_N (PF02771.22), Acyl-CoA_dh_M (PF02770.25), Acyl-CoA_dh_1 (PF00441.30), Acyl-CoA_dh_2 (PF08028.17), ACOX_C_alpha1 (PF22924.2). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQG1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable acyl-CoA dehydrogenase FadE25 |
| EC (curated) |
EC 1.3.99.-
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | fadE25 |
| eggNOG description | acyl-CoA dehydrogenase |
| Orthologous group | COG1960 |
| EC number |
EC 1.3.8.1
|
| KEGG orthology |
K00248
|
| KEGG pathways |
map00071, map00280, map00650, map01100, map01110, map01120, map01200, map01212
|
| Gene Ontology (13) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0016020, GO:0030312, GO:0044424, GO:0044444, GO:0044464 +1 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 | 0.324 · 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 |
|---|---|---|---|---|
Acyl-CoA_dh_N | PF02771.22 | 6.3e-31 | 17–125 | Acyl-CoA dehydrogenase, N-terminal domain |
Acyl-CoA_dh_M | PF02770.25 | 1.5e-28 | 132–226 | Acyl-CoA dehydrogenase, middle domain |
Acyl-CoA_dh_1 | PF00441.30 | 8.6e-50 | 238–388 | Acyl-CoA dehydrogenase, C-terminal domain |
Acyl-CoA_dh_2 | PF08028.17 | 1.7e-27 | 254–376 | Acyl-CoA dehydrogenase, C-terminal domain |
ACOX_C_alpha1 | PF22924.2 | 2.1e-06 | 271–388 | Acyl-CoA oxidase, C-alpha1 domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fixB (electron transfer flavoprotein subunit alpha), high confidence from genomic context alone (score 941 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3028c fixB |
electron transfer flavoprotein subunit alpha | 943 | 941 ctx | cooccurence:694 coexpression:559 experimental:419 |
Rv3029c fixA |
electron transfer flavoprotein subunit beta | 897 | 893 ctx | cooccurence:694 coexpression:432 experimental:418 |
Rv3276c purK |
5-(carboxyamino)imidazole ribonucleotide synthase | 855 | 855 ctx | neighborhood:849 |
Rv3275c purE |
5-(carboxyamino)imidazole ribonucleotide mutase | 853 | 854 ctx | neighborhood:849 |
Rv0860 fadB |
fatty oxidation protein FadB | 804 | 789 | coexpression:649 |
Rv3224 |
iron-regulated short-chain dehydrogenase/reductase | 747 | 747 | coexpression:624 |
Rv1078 pra hyp |
hypothetical protein | 746 | 746 | coexpression:746 |
Rv3442c rpsI |
30S ribosomal protein S9 | 703 | 703 | coexpression:703 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 654 | 640 | |
Rv0632c echA3 |
enoyl-CoA hydratase EchA3 | 652 | 640 | coexpression:425 |
Rv0636 hadB |
(3R)-hydroxyacyl-ACP dehydratase subunit HadB | 629 | 612 | |
Rv0951 sucC |
succinyl-CoA ligase subunit beta | 624 | 609 | coexpression:554 |
Rv0468 fadB2 |
3-hydroxybutyryl-CoA dehydrogenase | 714 | 602 | coexpression:427 |
Rv3774 echA21 |
enoyl-CoA hydratase EchA21 | 621 | 598 | |
Rv0637 hadC |
(3R)-hydroxyacyl-ACP dehydratase subunit HadC | 616 | 598 |
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
- MTBC0 PGAP product: acyl-CoA dehydrogenase
- Pfam (hmmscan --cut_ga): Acyl-CoA_dh_N PF02771.22 (E=6e-31), Acyl-CoA_dh_M PF02770.25 (E=2e-28), Acyl-CoA_dh_1 PF00441.30 (E=9e-50), Acyl-CoA_dh_2 PF08028.17 (E=2e-27), ACOX_C_alpha1 PF22924.2 (E=2e-06)
- (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_217791.1)
- 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), Acyl-CoA_dh_2 (PF08028.17), ACOX_C_alpha1 (PF22924.2)
- 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 P9WQG1 (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 —
127 functional partner(s); context anchor
fixB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003482|Rv3274c|fadE25 MVGWAGNPSFDLFKLPEEHDEMRSAIRALAEKEIAPHAAEVDEKARFPEEALVALNSSGFNAVHIPEEYGGQGADSVATCIVIEEVARVDASASLIPAVNKLGTMGLILRGSEELKKQVLPALAAEGAMASYALSEREAGSDAASMRTRAKADGDHWILNGAKCWITNGGKSTWYTVMAVTDPDRGANGISAFMVHKDDEGFTVGPKERKLGIKGSPTTELYFENCRIPGDRIIGEPGTGFKTALATLDHTRPTIGAQAVGIAQGALDAAIAYTKDRKQFGESISTFQAVQFMLADMAMKVEAARLMVYSAAARAERGEPDLGFISAASKCFASDVAMEVTTDAVQLFGGAGYTTDFPVERFMRDAKITQIYEGTNQIQRVVMSRALLR