fadE12 Resolved · high auto-curated
H37Rv Rv0972c · MTBC0 mtbc0_001038 ·
388 aa · 1089799–1090965 (-) ·
RefSeq NP_215487.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acyl-CoA dehydrogenase fadE12 |
|---|---|
| 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). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQG3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Acyl-CoA dehydrogenase FadE12 |
| EC (curated) |
EC 1.3.99.-
|
| Curated function | Has acyl-CoA dehydrogenase activity on a number of substrates. N-octanoyl-CoA is the best tested, but n-lauroyl-CoA, n-palmitoyl-CoA and isovaleryl-CoA were also used. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | fadE12 |
| eggNOG description | acyl-CoA dehydrogenase |
| Orthologous group | COG1960 |
| KEGG orthology |
K00257
|
| Gene Ontology (14) |
GO:0003674, GO:0003824, GO:0003995, GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0008152, GO:0016020, GO:0016491, GO:0016627, GO:0044464 +2 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 | 0.48 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 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 | 3.6e-28 | 9–119 | Acyl-CoA dehydrogenase, N-terminal domain |
Acyl-CoA_dh_M | PF02770.25 | 1.5e-16 | 124–204 | Acyl-CoA dehydrogenase, middle domain |
Acyl-CoA_dh_1 | PF00441.30 | 2.4e-30 | 239–380 | Acyl-CoA dehydrogenase, C-terminal domain |
Acyl-CoA_dh_2 | PF08028.17 | 1.4e-07 | 247–351 | Acyl-CoA dehydrogenase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: accA2 (acetyl/propionyl-CoA carboxylase subuit alpha), high confidence from genomic context alone (score 986 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0973c accA2 |
acetyl/propionyl-CoA carboxylase subuit alpha | 993 | 986 ctx | neighborhood:882 coexpression:874 textmining:584 |
Rv0974c accD2 |
acetyl-/propionyl-CoA carboxylase subunit beta | 992 | 986 ctx | neighborhood:881 coexpression:876 textmining:491 |
Rv0975c fadE13 |
acyl-CoA dehydrogenase FadE13 | 982 | 982 ctx | neighborhood:882 coexpression:800 |
Rv0976c hyp |
hypothetical protein | 961 | 960 ctx | neighborhood:881 cooccurence:487 |
Rv0971c echA7 |
enoyl-CoA hydratase EchA7 | 982 | 950 ctx | neighborhood:882 textmining:652 |
Rv3029c fixA |
electron transfer flavoprotein subunit beta | 815 | 808 ctx | cooccurence:470 coexpression:410 experimental:418 |
Rv0860 fadB |
fatty oxidation protein FadB | 819 | 794 | coexpression:657 |
Rv3028c fixB |
electron transfer flavoprotein subunit alpha | 797 | 789 ctx | cooccurence:412 coexpression:412 experimental:419 |
Rv3505 fadE27 |
acyl-CoA dehydrogenase FadE27 | 687 | 688 ctx | cooccurence:685 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 651 | 637 | |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 619 | 588 | database:459 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 616 | 585 | database:459 |
Rv1527c pks5 |
polyketide synthase | 616 | 585 | database:459 |
Rv2048c pks12 |
polyketide synthase | 615 | 584 | database:459 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 615 | 584 | database:459 |
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 fadE12
- MTBC0 PGAP product: acyl-CoA dehydrogenase
- Pfam (hmmscan --cut_ga): Acyl-CoA_dh_N PF02771.22 (E=4e-28), Acyl-CoA_dh_M PF02770.25 (E=1e-16), Acyl-CoA_dh_1 PF00441.30 (E=2e-30), Acyl-CoA_dh_2 PF08028.17 (E=1e-07)
- (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_215487.1)
- 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)
- 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 P9WQG3 (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
accA2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001038|Rv0972c|fadE12 MTDTSFIESEERQALRKAVASWVANYGHEYYLDKARKHEHTSELWAEAGKLGFLGVNLPEEYGGGGAGMYELSLVMEEMAAAGSALLLMVVSPAINGTIIAKFGTDDQKKRWLPGIADGSLTMAFAITEPDAGSNSHKITTTARRDGSDWIIKGQKVFISGIDQAQAVLVVGRSEEAKTGKLRPALFVVPTDAPGFSYTPIEMELVSPERQFQVFLDDVRLPADALVGAEDAAIAQLFAGLNPERIMGAASAVGMGRFALGRAVDYVKTRKVWSTPIGAHQGLAHPLAQCHIEVELAKLMTQKAATLYDHGDDFGAAEAANMAKYAAAEASSRAVDQAVQSMGGNGLTKEYGVAAMMTSARLARIAPISREMVLNFVAQTSLGLPRSY