fadE18 Family assigned · medium auto-curated
H37Rv Rv1933c · MTBC0 mtbc0_002047 ·
363 aa · 2202982–2204073 (-) ·
RefSeq NP_216449.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acyl-CoA dehydrogenase FadE18 |
|---|---|
| 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_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 |
P95281
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable acyl-CoA dehydrogenase FadE18 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | fadE18 |
| 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) pseudogene candidate
| pN/pS | 0.739 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 5.04% of strains (7314) · clonal |
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 | 1.6e-16 | 7–113 | Acyl-CoA dehydrogenase, N-terminal domain |
Acyl-CoA_dh_1 | PF00441.30 | 1.9e-36 | 214–358 | Acyl-CoA dehydrogenase, C-terminal domain |
Acyl-CoA_dh_2 | PF08028.17 | 6.7e-11 | 226–341 | Acyl-CoA dehydrogenase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadE17 (acyl-CoA dehydrogenase FadE17), high confidence from genomic context alone (score 963 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1934c fadE17 |
acyl-CoA dehydrogenase FadE17 | 984 | 963 ctx | neighborhood:782 cooccurence:773 textmining:586 |
Rv1935c echA13 |
enoyl-CoA hydratase EchA13 | 934 | 888 ctx | neighborhood:747 textmining:439 |
Rv3028c fixB |
electron transfer flavoprotein subunit alpha | 850 | 844 ctx | cooccurence:567 coexpression:412 experimental:419 |
Rv3560c fadE30 |
acyl-CoA dehydrogenase FadE30 | 849 | 844 ctx | fusion:420 cooccurence:740 |
Rv3029c fixA |
electron transfer flavoprotein subunit beta | 846 | 840 ctx | cooccurence:563 coexpression:406 experimental:418 |
Rv3562 fadE31 |
acyl-CoA dehydrogenase FadE31 | 859 | 816 ctx | cooccurence:738 |
Rv0860 fadB |
fatty oxidation protein FadB | 802 | 787 | coexpression:646 |
Rv3543c fadE29 |
acyl-CoA dehydrogenase FadE29 | 769 | 770 ctx | cooccurence:727 |
Rv1679 fadE16 |
acyl-CoA dehydrogenase FadE16 | 768 | 768 ctx | cooccurence:766 |
Rv3504 fadE26 |
acyl-CoA dehydrogenase FadE26 | 797 | 745 ctx | cooccurence:728 |
Rv0131c fadE1 |
acyl-CoA dehydrogenase FadE1 | 735 | 735 ctx | cooccurence:735 |
Rv3797 fadE35 |
acyl-CoA dehydrogenase FadE35 | 721 | 721 ctx | cooccurence:720 |
Rv2766c |
short-chain type dehydrogenase/reductase | 707 | 697 ctx | neighborhood:544 |
Rv1937 |
oxygenase | 703 | 684 ctx | neighborhood:479 |
Rv1346 mbtN |
acyl-[acyl-carrier-protein | 661 | 661 ctx | cooccurence:659 |
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 FadE18
- MTBC0 PGAP product: acyl-CoA dehydrogenase family protein
- Pfam (hmmscan --cut_ga): Acyl-CoA_dh_N PF02771.22 (E=2e-16), Acyl-CoA_dh_1 PF00441.30 (E=2e-36), Acyl-CoA_dh_2 PF08028.17 (E=7e-11)
- (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_216449.1)
- Domains: Pfam-A via hmmscan --cut_ga — Acyl-CoA_dh_N (PF02771.22), 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 P95281 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
124 functional partner(s); context anchor
fadE17 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002047|Rv1933c|fadE18 MDFRYSTEQDDFRASLRGFLGRGAPVREMAAADGSDRRLWQRLCTELELPALHVPPEHGGLGATLVETAIAFAELGRALTPIPFAATVFAIEAILRMGDDEQRKRLLAGLLTGARIGTIAVSGHDVASATTVRAVRRDGRPALTGECTPVLHGHVADLFVVPAVADGSIVLHVVAADAPGVTVTPLPSFDITRPVATLRLAGSPAEPLTAGTPDDMERVLDVARVLLAAEMLGGAEACLDLAVQYAGRRTQFDRPIGSFQAVKHACADMMIEIDATRATVMFAAMSAANGDELQTVAPLAKAQTAETFVLCAGSALQIHGAIAFTWEHDLHLYYRRAKTTEALFGSSARNRALLAERAGLVKA