fadE1 Resolved · high auto-curated
H37Rv Rv0131c · MTBC0 - ·
447 aa · 158315–159658 (-) ·
RefSeq NP_214645.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acyl-CoA dehydrogenase FadE1 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Acyl-CoA dehydrogenase FadE1. 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.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P96808
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable acyl-CoA dehydrogenase FadE1 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | fadE1 |
| eggNOG description | acyl-CoA dehydrogenase |
| Orthologous group | COG1960 |
| EC number |
EC 1.3.8.7
|
| KEGG orthology |
K00249
|
| KEGG pathways |
map00071, map00280, map00410, map00640, map01100, map01110, map01130, map01200, map01212, map03320
|
| KEGG modules |
M00013, M00036, M00087
|
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 | 0.576 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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 | 1.4e-13 | 27–141 | Acyl-CoA dehydrogenase, N-terminal domain |
Acyl-CoA_dh_M | PF02770.25 | 3.3e-22 | 145–232 | Acyl-CoA dehydrogenase, middle domain |
Acyl-CoA_dh_1 | PF00441.30 | 1.5e-30 | 261–409 | Acyl-CoA dehydrogenase, C-terminal domain |
Acyl-CoA_dh_2 | PF08028.17 | 5.4e-08 | 275–380 | Acyl-CoA dehydrogenase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadE36 (acyl-CoA dehydrogenase FadE36), high confidence from genomic context alone (score 977 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3761c fadE36 |
acyl-CoA dehydrogenase FadE36 | 977 | 977 ctx | fusion:899 cooccurence:725 |
Rv2790c ltp1 |
lipid-transfer protein | 943 | 941 | database:900 |
Rv0860 fadB |
fatty oxidation protein FadB | 928 | 922 | coexpression:647 database:750 |
Rv2502c accD1 |
acetyl-/propionyl-CoA carboxylase subunit beta | 925 | 922 | database:900 |
Rv0400c fadE7 |
acyl-CoA dehydrogenase FadE7 | 912 | 912 | database:900 |
Rv2486 echA14 |
enoyl-CoA hydratase EchA14 | 851 | 846 | database:750 |
Rv3373 echA18 |
enoyl-CoA hydratase | 851 | 846 | database:750 |
Rv3516 echA19 |
enoyl-CoA hydratase EchA19 | 852 | 845 | database:750 |
Rv1070c echA8 |
enoyl-CoA hydratase EchA8 | 851 | 845 | database:750 |
Rv0456c echA2 |
enoyl-CoA hydratase EchA2 | 851 | 845 | database:750 |
Rv1071c echA9 |
enoyl-CoA hydratase EchA9 | 850 | 845 | database:750 |
Rv1141c echA11 |
enoyl-CoA hydratase EchA11 | 850 | 845 | database:750 |
Rv0632c echA3 |
enoyl-CoA hydratase EchA3 | 850 | 845 | database:750 |
Rv2831 echA16 |
enoyl-CoA hydratase EchA16 | 850 | 845 | database:750 |
Rv0971c echA7 |
enoyl-CoA hydratase EchA7 | 850 | 845 | database:750 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): acyl-CoA dehydrogenase FadE1
- Pfam (hmmscan --cut_ga): Acyl-CoA_dh_N PF02771.22 (E=1e-13), Acyl-CoA_dh_M PF02770.25 (E=3e-22), Acyl-CoA_dh_1 PF00441.30 (E=1e-30), Acyl-CoA_dh_2 PF08028.17 (E=5e-08)
- (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_214645.1)
- 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 P96808 (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 —
125 functional partner(s); context anchor
fadE36 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0131c|fadE1 MPVRRRAGERLPTVWDFETDPQYQSKLDWVEKFMAEELEPLDLVALDPYDKKNADTMAILRPLQRQVKDQGLWAAHLRPELGGQGFGQVKLALLNEIIGRSRWAPSAFGCQAPDSGNAEILALFGTDEQKARYLRPLLDGEITSCYSMTEPQGGSDPGLFVTAATRDAAGNGDWIINGEKWFSTNAKHASFFIVMAVTKPEARTYEKMSLFIVPADTPGIEIVRNVGVGAESTRHASHGYIRYHDVRVPADHVLGGEGQAFMIAQTRLGGGRIHHAMRTIALARRAFDMMCERALSRQTRHGRLADLQMTQEKIADSWIQIEQFRLLVLRTAWLIDKHHDYQKVRRDIAAVKVAMPQVLHDVVQRAMHLHGALGVSDEMPFVKMMLAAESLGIADGATELHKMTVARRTLREYQPVTTLFPSQHIPTRRAHAEAWLAQRLEHAIAEF