fadE24 Family assigned · medium auto-curated
H37Rv Rv3139 · MTBC0 mtbc0_003337 ·
468 aa · 3528065–3529471 (+) ·
RefSeq NP_217655.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acyl-CoA dehydrogenase |
|---|---|
| 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_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 |
P95187
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable acyl-CoA dehydrogenase FadE24 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | fadE24 |
| eggNOG description | acyl-CoA dehydrogenase |
| Orthologous group | COG1960 |
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 | 3.247 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 9 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 | 2.1e-21 | 111–220 | Acyl-CoA dehydrogenase, N-terminal domain |
Acyl-CoA_dh_M | PF02770.25 | 4.1e-13 | 228–314 | Acyl-CoA dehydrogenase, middle domain |
Acyl-CoA_dh_1 | PF00441.30 | 5.7e-29 | 337–464 | Acyl-CoA dehydrogenase, C-terminal domain |
Acyl-CoA_dh_2 | PF08028.17 | 3.1e-12 | 345–460 | Acyl-CoA dehydrogenase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadE23 (acyl-CoA dehydrogenase FadE23), high confidence from genomic context alone (score 985 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3140 fadE23 |
acyl-CoA dehydrogenase FadE23 | 994 | 985 ctx | neighborhood:853 coexpression:860 textmining:637 |
Rv3029c fixA |
electron transfer flavoprotein subunit beta | 834 | 827 ctx | cooccurence:523 coexpression:410 experimental:418 |
Rv3028c fixB |
electron transfer flavoprotein subunit alpha | 828 | 822 ctx | cooccurence:504 coexpression:414 experimental:419 |
Rv0860 fadB |
fatty oxidation protein FadB | 849 | 821 | coexpression:647 |
Rv3138 pflA |
pyruvate formate lyase activating protein PflA | 829 | 788 ctx | neighborhood:785 |
Rv1679 fadE16 |
acyl-CoA dehydrogenase FadE16 | 743 | 744 ctx | cooccurence:737 |
Rv0243 fadA2 |
acetyl-CoA acetyltransferase FadA | 706 | 668 | coexpression:577 |
Rv0241c htdX |
3-hydroxyacyl-thioester dehydratase HtdX | 651 | 651 | |
Rv1346 mbtN |
acyl-[acyl-carrier-protein | 644 | 644 ctx | cooccurence:637 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 649 | 635 | |
Rv3563 fadE32 |
acyl-CoA dehydrogenase FadE32 | 653 | 612 ctx | cooccurence:602 |
Rv3141 fadB4 |
NADPH quinone oxidoreductase FadB | 793 | 606 ctx | neighborhood:548 textmining:498 |
Rv3137 hisN |
histidinol-phosphatase | 662 | 606 ctx | neighborhood:602 |
Rv2524c fas |
fatty acid synthase | 648 | 600 | |
Rv1527c pks5 |
polyketide synthase | 619 | 588 | 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
- MTBC0 PGAP product: acyl-CoA dehydrogenase family protein
- Pfam (hmmscan --cut_ga): Acyl-CoA_dh_N PF02771.22 (E=2e-21), Acyl-CoA_dh_M PF02770.25 (E=4e-13), Acyl-CoA_dh_1 PF00441.30 (E=6e-29), Acyl-CoA_dh_2 PF08028.17 (E=3e-12)
- (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_217655.1)
- 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 P95187 (TrEMBL, unreviewed; 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
fadE23 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003337|Rv3139|fadE24 MTNTTSAANAAKPSGARTDRRGRTTGVGLAPHKRTGIDVALALLTPIVGQEFLDKYRLRDPLNRSLRYGVKTMFATAGAATRQFQRVQGLRGGPTRLKSSGRDYFDLTPDDDQKLIIETVDEFAEEVLRPAAHDADDAATYPSDLTAKAAELGITAINIPEDFDGIAEHRSSVTNVLVAEALAYGDMGLALPILAPGGVASALTHWGSADQQATYLKEFAGENVPQACVAITEPQPLFDPTRLKTTAVRTPSGYRLDGVKSLIPAAADAELFIVGAQLGGKPALFIVESAASGLTVKADPSMGIRGAALGQVELCGVSVPLNARLGEDEASDNDYSEALALARLGWAALAVGTSHAVLDYVVPYVKQRQAFGEPIAHRQAVAFMCANIAIELDGLRLITWRGASRAEQGLPFAREAALAKRLGSDKGMQIGLDGVQLLGGHGYTKEHPVERWYRDLRAIGVAEGVVVI