Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acyl-CoA dehydrogenase FadE4 |
|---|
| MTBC0 PGAP re-annotation | acyl-CoA dehydrogenase family protein |
|---|
| Revised (this work) | Acyl-CoA dehydrogenase family protein. Pfam: 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 |
P96414
TrEMBL · unreviewed
· Evidence at protein level
|
|---|
| UniProt name | Probable acyl-CoA dehydrogenase FadE4 |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|
| Preferred name | fadE4 |
|---|
| 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 |
0.421 · purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
6 synonymous, 8 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_1 | PF00441.30 |
3.7e-11 | 238–385 |
Acyl-CoA dehydrogenase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv2790c ltp1 |
lipid-transfer protein |
953 |
951 |
database:900 |
Rv0860 fadB |
fatty oxidation protein FadB |
932 |
922 |
coexpression:645 database:750 |
Rv2502c accD1 |
acetyl-/propionyl-CoA carboxylase subunit beta |
924 |
921 |
database:900 |
Rv0400c fadE7 |
acyl-CoA dehydrogenase FadE7 |
900 |
900 |
database:900 |
Rv0456c echA2 |
enoyl-CoA hydratase EchA2 |
853 |
848 |
database:750 |
Rv2831 echA16 |
enoyl-CoA hydratase EchA16 |
851 |
846 |
database:750 |
Rv3373 echA18 |
enoyl-CoA hydratase |
851 |
846 |
database:750 |
Rv1070c echA8 |
enoyl-CoA hydratase EchA8 |
851 |
845 |
database:750 |
Rv3039c echA17 |
enoyl-CoA hydratase EchA17 |
850 |
845 |
database:750 |
Rv0632c echA3 |
enoyl-CoA hydratase EchA3 |
850 |
845 |
database:750 |
Rv3774 echA21 |
enoyl-CoA hydratase EchA21 |
850 |
845 |
database:750 |
Rv1472 echA12 |
enoyl-CoA hydratase EchA12 |
850 |
845 |
database:750 |
Rv1071c echA9 |
enoyl-CoA hydratase EchA9 |
850 |
845 |
database:750 |
Rv1141c echA11 |
enoyl-CoA hydratase EchA11 |
850 |
845 |
database:750 |
Rv2679 echA15 |
enoyl-CoA hydratase EchA15 |
850 |
844 |
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
- Legacy H37Rv annotation: acyl-CoA dehydrogenase FadE4
- MTBC0 PGAP product: acyl-CoA dehydrogenase family protein
- Pfam (hmmscan --cut_ga): Acyl-CoA_dh_1 PF00441.30 (E=4e-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_214745.1)
- Domains: Pfam-A via hmmscan --cut_ga — 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
P96414
(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 —
121 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000246|Rv0231|fadE4
MLLNPNHLTRKYPDRRSGEIMAATVDFFESRGKARLKHDDHERIWYSDFLDFVGRERIFASLLTPASYGADDCRWDTYRISEFAEIMGFYGLSYWYPFQVTALGLGPIWMSANEDAKRKAAAGLEAGEVFAFGLSEQTHGADVYQTDMILTPSDGGWTANGEKYYIGNANVARMVSTFGKIAGTPESQEYVFFVADSQHERYDLIKNVVNSQNYVANYALRDYPVTEADILHRGAEAFHAALNTVNVCKYNLGWGAIGMCTHALYESVTHAANRHLYGTVVTDFSHVRRLLTDAYVRLIAMKLVASRASDYMRSASAADRRYLLYSPLTKAKVTSEGERVITALWDVIAAKGVEKDTFFETVAREIGLLPRLEGTVHINIGLLGKFMPNYLFAPDSTLPVIPRRDDAADDAFLFAQGPTGGLGKVRFHDWRASFDTCAHLPNVALLREQVDVFAELLASATPDAAQQKDIDFAFGVGQLFANVPYAQLILEEARLSGVDEALIDEIFGVLVRDFNTHAVELHGRSATTAEQARFAMRMVRRPVHDPARYDQIWKDHVLALNGAYQMAP
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