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 |
P9WQF7
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | Probable acyl-CoA dehydrogenase FadE10 |
|---|
| EC (curated) |
EC 1.3.-.-
|
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|
| Preferred name | fadE10 |
|---|
| eggNOG description | acyl-CoA dehydrogenase |
|---|
| Orthologous group | COG1960 |
|---|
| Gene Ontology (13) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0016020, GO:0030312, GO:0044424, GO:0044444, GO:0044464 +1 more
|
|---|
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 |
0.08 · strong purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
55 synonymous, 12 missense, 1 nonsense, 0 frameshift
|
|---|
| Disruption |
1 distinct premature-stop/frameshift site(s); most common in
0.78% of strains
(1135) · 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 |
2.0e-19 | 63–163 |
Acyl-CoA dehydrogenase, N-terminal domain |
Acyl-CoA_dh_M | PF02770.25 |
1.3e-20 | 167–263 |
Acyl-CoA dehydrogenase, middle domain |
Acyl-CoA_dh_1 | PF00441.30 |
7.4e-32 | 277–435 |
Acyl-CoA dehydrogenase, C-terminal domain |
Acyl-CoA_dh_2 | PF08028.17 |
5.4e-05 | 296–398 |
Acyl-CoA dehydrogenase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv0860 fadB |
fatty oxidation protein FadB |
804 |
788 |
coexpression:648 |
Rv3028c fixB |
electron transfer flavoprotein subunit alpha |
713 |
701 |
coexpression:424 experimental:419 |
Rv3029c fixA |
electron transfer flavoprotein subunit beta |
709 |
697 |
coexpression:412 experimental:418 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I |
651 |
637 |
|
Rv0632c echA3 |
enoyl-CoA hydratase EchA3 |
606 |
591 |
|
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase |
615 |
585 |
database:459 |
Rv1070c echA8 |
enoyl-CoA hydratase EchA8 |
599 |
585 |
|
Rv2940c mas |
multifunctional mycocerosic acid synthase |
615 |
584 |
database:459 |
Rv1527c pks5 |
polyketide synthase |
614 |
583 |
database:459 |
Rv2048c pks12 |
polyketide synthase |
614 |
583 |
database:459 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC |
613 |
583 |
database:459 |
Rv0905 echA6 |
enoyl-CoA hydratase EchA6 |
593 |
578 |
|
Rv3774 echA21 |
enoyl-CoA hydratase EchA21 |
593 |
578 |
|
Rv1071c echA9 |
enoyl-CoA hydratase EchA9 |
592 |
578 |
|
Rv0456c echA2 |
enoyl-CoA hydratase EchA2 |
592 |
577 |
|
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-19), Acyl-CoA_dh_M PF02770.25 (E=1e-20), Acyl-CoA_dh_1 PF00441.30 (E=7e-32), Acyl-CoA_dh_2 PF08028.17 (E=5e-05)
- (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_215388.1)
- 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
P9WQF7
(SwissProt, reviewed; 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 —
106 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000928|Rv0873|fadE10
MAQQTQVTEEQARALAEESRESGWDKPSFAKELFLGRFPLGLIHPFPKPSDAEEARTEAFLVKLREFLDTVDGSVIERAAQIPDEYVKGLAELGCFGLKIPSEYGGLNMSQVAYNRVLMMVTTVHSSLGALLSAHQSIGVPEPLKLAGTAEQKRRFLPRCAAGAISAFLLTEPDVGSDPARMASTATPIDDGQAYELEGVKLWTTNGVVADLLVVMARVPRSEGHRGGISAFVVEADSPGITVERRNKFMGLRGIENGVTRLHRVRVPKDNLIGREGDGLKIALTTLNAGRLSLPAIATGVAKQALKIAREWSVERVQWGKPVGQHEAVASKISFIAATNYALDAVVELSSQMADEGRNDIRIEAALAKLWSSEMACLVGDELLQIRGGRGYETAESLAARGERAVPVEQMVRDLRINRIFEGSSEIMRLLIAREAVDAHLTAAGDLANPKADLRQKAAAAAGASGFYAKWLPKLVFGEGQLPTTYREFGALATHLRFVERSSRKLARNTFYGMARWQASLEKKQGFLGRIVDIGAELFAISAACVRAEAQRTADPVEGEQAYELAEAFCQQATLRVEALFDALWSNTDSIDVRLANDVLEGRYTWLEQGILDQSEGTGPWIASWEPGPSTEANLARRFLTVSPSSEAKL
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