fadE17 Resolved · high auto-curated
H37Rv Rv1934c · MTBC0 mtbc0_002048 ·
409 aa · 2204075–2205304 (-) ·
RefSeq NP_216450.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acyl-CoA dehydrogenase FadE17 |
|---|---|
| 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). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95280
SwissProt · reviewed
· Evidence at transcript level
|
|---|---|
| UniProt name | Putative acyl-CoA dehydrogenase FadE17 |
| EC (curated) |
EC 1.3.99.-
|
UniProt still lists this protein as Putative acyl-CoA dehydrogenase FadE17; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | fadE17 |
| eggNOG description | acyl-CoA dehydrogenase |
| Orthologous group | COG1960 |
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.799 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 11 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 | 6.1e-22 | 7–124 | Acyl-CoA dehydrogenase, N-terminal domain |
Acyl-CoA_dh_M | PF02770.25 | 1.0e-20 | 128–220 | Acyl-CoA dehydrogenase, middle domain |
Acyl-CoA_dh_1 | PF00441.30 | 2.7e-20 | 234–397 | Acyl-CoA dehydrogenase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: echA13 (enoyl-CoA hydratase EchA13), high confidence from genomic context alone (score 991 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1935c echA13 |
enoyl-CoA hydratase EchA13 | 993 | 991 ctx | neighborhood:869 coexpression:900 |
Rv1933c fadE18 |
acyl-CoA dehydrogenase FadE18 | 984 | 963 ctx | neighborhood:782 cooccurence:773 textmining:586 |
Rv3564 fadE33 |
acyl-CoA dehydrogenase FadE33 | 925 | 834 ctx | cooccurence:773 textmining:571 |
Rv1966 mce3A |
Mce family protein Mce3A | 804 | 804 | coexpression:804 |
Rv1965 yrbE3B |
integral membrane protein | 788 | 788 | coexpression:788 |
Rv0860 fadB |
fatty oxidation protein FadB | 802 | 786 | coexpression:645 |
Rv3563 fadE32 |
acyl-CoA dehydrogenase FadE32 | 834 | 784 ctx | cooccurence:755 |
Rv1968 mce3C |
Mce family protein Mce3C | 780 | 780 | coexpression:780 |
Rv3029c fixA |
electron transfer flavoprotein subunit beta | 769 | 759 | coexpression:406 experimental:418 |
Rv1969 mce3D |
Mce family protein Mce3D | 754 | 754 | coexpression:754 |
Rv3028c fixB |
electron transfer flavoprotein subunit alpha | 763 | 753 | coexpression:412 experimental:419 |
Rv1937 |
oxygenase | 763 | 749 ctx | neighborhood:528 |
Rv3505 fadE27 |
acyl-CoA dehydrogenase FadE27 | 808 | 739 ctx | cooccurence:738 |
Rv1967 mce3B |
Mce family protein Mce3B | 734 | 734 | coexpression:734 |
Rv1679 fadE16 |
acyl-CoA dehydrogenase FadE16 | 706 | 706 ctx | cooccurence:702 |
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 FadE17
- MTBC0 PGAP product: acyl-CoA dehydrogenase
- Pfam (hmmscan --cut_ga): Acyl-CoA_dh_N PF02771.22 (E=6e-22), Acyl-CoA_dh_M PF02770.25 (E=1e-20), Acyl-CoA_dh_1 PF00441.30 (E=3e-20)
- (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_216450.1)
- 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 P95280 (SwissProt, reviewed; Evidence at transcript 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 —
129 functional partner(s); context anchor
echA13 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002048|Rv1934c|fadE17 MDVSYPPEAEAFRDRIREFVAEHLPPGWPGPGALPPHEREEFARHWRRALAGAGLVAVSWPTEYGGGGLSPMEQVVLAEEFARAGAPERAENDLLGIDLLGNTLIALGSEAQKRHFLPRILSGEHRWCQGFSEPEAGSDLASVRTRGVLDGDEWVINGHKIWTSAGTTANWIFLLARTDPSAAKHRGLSFLLVPMDQPGVVVRPIVNAAGHSSFSEVFLTDARTSAGNVVGRVGDGWSTAMTLLGFERGSHIATAAIDFERDLQRLCELARDRGLHTDPRVRDGLAWCYARVQIMRYRGYRDLTLALTGRPPGAEAAITKVIWSEYFRRYTDLAVEILGLEALGPRGPGNGGARLVPEAGTPNSPACWMDELLYARAATIYAGSSQIQRNVIGERLLGLPKEPRPEVLC