fadE7 Resolved · high auto-curated
H37Rv Rv0400c · MTBC0 mtbc0_000420 ·
395 aa · 481930–483117 (-) ·
RefSeq NP_214914.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acyl-CoA dehydrogenase FadE7 |
|---|---|
| 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), 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 |
P95208
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Acyl-CoA dehydrogenase FadE7 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | fadE7 |
| eggNOG description | acyl-CoA dehydrogenase |
| Orthologous group | COG1960 |
| EC number |
EC 1.3.8.6
|
| KEGG orthology |
K00252
|
| KEGG pathways |
map00071, map00310, map00362, map00380, map01100, map01120, map01130
|
| KEGG modules |
M00032
|
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 | 1.577 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 | 6.4e-31 | 23–135 | Acyl-CoA dehydrogenase, N-terminal domain |
Acyl-CoA_dh_M | PF02770.25 | 3.9e-25 | 139–229 | Acyl-CoA dehydrogenase, middle domain |
Acyl-CoA_dh_1 | PF00441.30 | 5.0e-29 | 241–386 | Acyl-CoA dehydrogenase, C-terminal domain |
Acyl-CoA_dh_2 | PF08028.17 | 3.2e-08 | 257–367 | Acyl-CoA dehydrogenase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lpqK (lipoprotein LpqK), high confidence from genomic context alone (score 887 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2790c ltp1 |
lipid-transfer protein | 943 | 942 | database:900 |
Rv0975c fadE13 |
acyl-CoA dehydrogenase FadE13 | 923 | 923 | database:900 |
Rv0860 fadB |
fatty oxidation protein FadB | 928 | 922 | coexpression:647 database:750 |
Rv3140 fadE23 |
acyl-CoA dehydrogenase FadE23 | 916 | 917 | database:900 |
Rv2215 dlaT |
pyruvate dehydrogenase E2 component dihydrolipoamide acyltransferase | 917 | 915 | database:900 |
Rv0131c fadE1 |
acyl-CoA dehydrogenase FadE1 | 912 | 912 | database:900 |
Rv0154c fadE2 |
acyl-CoA dehydrogenase FadE2 | 905 | 906 | database:900 |
Rv0462 lpdC |
dihydrolipoamide dehydrogenase | 906 | 905 | database:900 |
Rv0231 fadE4 |
acyl-CoA dehydrogenase FadE4 | 900 | 900 | database:900 |
Rv0398c hyp |
hypothetical protein | 887 | 887 ctx | neighborhood:881 |
Rv0399c lpqK |
lipoprotein LpqK | 887 | 887 ctx | neighborhood:882 |
Rv1071c echA9 |
enoyl-CoA hydratase EchA9 | 870 | 866 | database:750 |
Rv0632c echA3 |
enoyl-CoA hydratase EchA3 | 867 | 862 | database:750 |
Rv0673 echA4 |
enoyl-CoA hydratase EchA4 | 854 | 849 | database:750 |
Rv0675 echA5 |
enoyl-CoA hydratase EchA5 | 853 | 846 | 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 FadE7
- MTBC0 PGAP product: acyl-CoA dehydrogenase
- Pfam (hmmscan --cut_ga): Acyl-CoA_dh_N PF02771.22 (E=6e-31), Acyl-CoA_dh_M PF02770.25 (E=4e-25), Acyl-CoA_dh_1 PF00441.30 (E=5e-29), Acyl-CoA_dh_2 PF08028.17 (E=3e-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_214914.1)
- 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 P95208 (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 —
123 functional partner(s); context anchor
lpqK - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000420|Rv0400c|fadE7 MSTPTPPALDRDDPLGLDASLSSDEIAVRDTVRRFCAEHVTPHVAAWFEDGDLPVARDLAKQFGELGLLGMQLHGHGCGGASAVHYGLACRELEAADSGIRSLVSVQGSLAMFAIASFGSDEQKRQWLPGMATGDLLGCFGLTEPDVGSDPAAMKTRARRDGPDWVITGGKMWITNGSVADVAIVWAATDDGIRGFIVPTDTPGFTANTIGHKLSLRASITSELVLDNVRLPADAMLPGATGLRAPLACLSEARYGIVWGAMGAARSAWQCALDYARQRTQFGRPIAGFQLTQAKLVDMAVELHKGQLLSLHLGRLKDRVGLRPDQVSFGKLNNTREALKICRTARTILGGNGISLEYPVIRHMVNLESVLTYEGTPEMHQLVLGQAFTGLAAFR