fadE13 Family assigned · medium auto-curated
H37Rv Rv0975c · MTBC0 mtbc0_001041 ·
382 aa · 1094563–1095711 (-) ·
RefSeq NP_215490.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acyl-CoA dehydrogenase FadE13 |
|---|---|
| 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 |
O86319
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable acyl-CoA dehydrogenase FadE13 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | fadE13 |
| 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 | 0.531 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.15% of strains (218) · 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 | 1.8e-22 | 6–119 | Acyl-CoA dehydrogenase, N-terminal domain |
Acyl-CoA_dh_M | PF02770.25 | 1.2e-24 | 123–217 | Acyl-CoA dehydrogenase, middle domain |
Acyl-CoA_dh_1 | PF00441.30 | 3.5e-44 | 229–378 | Acyl-CoA dehydrogenase, C-terminal domain |
Acyl-CoA_dh_2 | PF08028.17 | 1.2e-13 | 245–360 | Acyl-CoA dehydrogenase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: accD2 (acetyl-/propionyl-CoA carboxylase subunit beta), high confidence from genomic context alone (score 988 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0974c accD2 |
acetyl-/propionyl-CoA carboxylase subunit beta | 989 | 988 ctx | neighborhood:881 coexpression:888 |
Rv0976c hyp |
hypothetical protein | 986 | 986 ctx | neighborhood:881 coexpression:859 |
Rv0973c accA2 |
acetyl/propionyl-CoA carboxylase subuit alpha | 984 | 984 ctx | neighborhood:882 coexpression:856 |
Rv0971c echA7 |
enoyl-CoA hydratase EchA7 | 982 | 982 ctx | neighborhood:882 database:750 |
Rv0972c fadE12 |
acyl-CoA dehydrogenase fadE12 | 982 | 982 ctx | neighborhood:882 coexpression:800 |
Rv2790c ltp1 |
lipid-transfer protein | 943 | 941 | database:900 |
Rv0860 fadB |
fatty oxidation protein FadB | 940 | 936 | coexpression:661 database:750 |
Rv0400c fadE7 |
acyl-CoA dehydrogenase FadE7 | 923 | 923 | database:900 |
Rv2502c accD1 |
acetyl-/propionyl-CoA carboxylase subunit beta | 925 | 922 | database:900 |
Rv3028c fixB |
electron transfer flavoprotein subunit alpha | 884 | 879 ctx | cooccurence:607 coexpression:411 experimental:419 |
Rv3029c fixA |
electron transfer flavoprotein subunit beta | 865 | 860 ctx | cooccurence:615 coexpression:408 experimental:418 |
Rv0675 echA5 |
enoyl-CoA hydratase EchA5 | 852 | 845 | database:750 |
Rv3516 echA19 |
enoyl-CoA hydratase EchA19 | 852 | 845 | database:750 |
Rv3550 echA20 |
enoyl-CoA hydratase EchA20 | 850 | 845 | database:750 |
Rv0456c echA2 |
enoyl-CoA hydratase EchA2 | 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
- Legacy H37Rv annotation: acyl-CoA dehydrogenase FadE13
- MTBC0 PGAP product: acyl-CoA dehydrogenase family protein
- Pfam (hmmscan --cut_ga): Acyl-CoA_dh_N PF02771.22 (E=2e-22), Acyl-CoA_dh_M PF02770.25 (E=1e-24), Acyl-CoA_dh_1 PF00441.30 (E=3e-44), Acyl-CoA_dh_2 PF08028.17 (E=1e-13)
- (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_215490.1)
- 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 O86319 (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 —
120 functional partner(s); context anchor
accD2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001041|Rv0975c|fadE13 MNIWTTPERQQLRKTVRAFAEREILPHVDEWERIGELPRGLHRLAGAAGLLGAGFPEAVGGGGGDGADPVIICEEMHQAGAPGGVYASLFTCGIAVPHMVASGDERLIATYVRPTLAGEKIGALAITEPGGGSDVGHLRTSAVRDGDHYVINGAKTYITSGVRADYVVTAVRTGGPGAAGVSLLVVEKDTPGFEVTRKLDKMGWRSSDTAELCYTDVAVPATNLVGAENSGFTQIARAFVSERIGLAAQAYSSAQRCLDLTAQWCRDRETFGRPLISRQSVQNTLAEMARRIDVARVYAHHVVERQLAGETDLIAQVCFAKNTAVQAGEWVANQAVQLFGGMGYMAESEVERQYRDMRILGIGGGTTEILTALAAKTLGYQS