fadE19 Family assigned · medium auto-curated
H37Rv Rv2500c · MTBC0 mtbc0_002662 ·
394 aa · 2836617–2837801 (-) ·
RefSeq NP_217016.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acyl-CoA dehydrogenase FadE19 |
|---|---|
| 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 |
I6Y0W5
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible acyl-CoA dehydrogenase FadE19 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | fadE19 |
| eggNOG description | acyl-CoA dehydrogenase |
| Orthologous group | COG1960 |
| EC number |
EC 1.3.8.1, EC 1.3.99.12
|
| KEGG orthology |
K00248, K11410
|
| KEGG pathways |
map00071, map00280, map00650, map01100, map01110, map01120, map01200, map01212
|
| Gene Ontology (112) |
GO:0000062, GO:0000166, GO:0003674, GO:0003824, GO:0003995, GO:0004085, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005739 +100 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 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 | 3.5e-39 | 15–125 | Acyl-CoA dehydrogenase, N-terminal domain |
Acyl-CoA_dh_M | PF02770.25 | 6.8e-22 | 131–230 | Acyl-CoA dehydrogenase, middle domain |
Acyl-CoA_dh_1 | PF00441.30 | 6.3e-49 | 243–391 | Acyl-CoA dehydrogenase, C-terminal domain |
Acyl-CoA_dh_2 | PF08028.17 | 1.5e-18 | 259–374 | Acyl-CoA dehydrogenase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2499c (oxidase regulatory-like protein), high confidence from genomic context alone (score 990 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2499c |
oxidase regulatory-like protein | 998 | 990 ctx | neighborhood:881 coexpression:844 textmining:815 |
Rv2498c citE |
citrate (pro-3S)-lyase subunit beta | 995 | 977 ctx | neighborhood:881 coexpression:787 textmining:830 |
Rv2501c accA1 |
acetyl/propionyl-CoA carboxylase subuit alpha | 974 | 973 ctx | neighborhood:881 coexpression:767 |
Rv2502c accD1 |
acetyl-/propionyl-CoA carboxylase subunit beta | 982 | 930 ctx | neighborhood:881 coexpression:433 textmining:764 |
Rv3028c fixB |
electron transfer flavoprotein subunit alpha | 928 | 925 ctx | cooccurence:713 coexpression:410 experimental:419 |
Rv0860 fadB |
fatty oxidation protein FadB | 928 | 922 | coexpression:647 database:750 |
Rv3029c fixA |
electron transfer flavoprotein subunit beta | 905 | 901 ctx | cooccurence:729 coexpression:406 experimental:418 |
Rv2503c scoB |
succinyl-CoA:3-ketoacid-CoA transferase subunit B | 929 | 894 ctx | neighborhood:881 |
Rv2504c scoA |
succinyl-CoA:3-ketoacid-CoA transferase subunit A | 914 | 891 ctx | neighborhood:881 |
Rv0675 echA5 |
enoyl-CoA hydratase EchA5 | 852 | 845 | database:750 |
Rv0673 echA4 |
enoyl-CoA hydratase EchA4 | 851 | 845 | database:750 |
Rv1935c echA13 |
enoyl-CoA hydratase EchA13 | 851 | 845 | database:750 |
Rv3550 echA20 |
enoyl-CoA hydratase EchA20 | 850 | 845 | database:750 |
Rv0971c echA7 |
enoyl-CoA hydratase EchA7 | 850 | 845 | database:750 |
Rv0222 echA1 |
enoyl-CoA hydratase EchA1 | 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 FadE19
- MTBC0 PGAP product: acyl-CoA dehydrogenase family protein
- Pfam (hmmscan --cut_ga): Acyl-CoA_dh_N PF02771.22 (E=3e-39), Acyl-CoA_dh_M PF02770.25 (E=7e-22), Acyl-CoA_dh_1 PF00441.30 (E=6e-49), Acyl-CoA_dh_2 PF08028.17 (E=1e-18)
- (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_217016.1)
- 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 I6Y0W5 (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 —
116 functional partner(s); context anchor
Rv2499c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002662|Rv2500c|fadE19 MTTTTTTISGGILPKEYQDLRDTVADFARTVVAPVSAKHDAEHSFPYEIVAKMGEMGLFGLPFPEEYGGMGGDYFALSLVLEELGKVDQSVAITLEAAVGLGAMPIYRFGTEEQKQKWLPDLTSGRALAGFGLTEPGAGSDAGSTRTTARLEGDEWIINGSKQFITNSGTDITSLVTVTAVTGTTGTAADAKKEISTIIVPSGTPGFTVEPVYNKVGWNASDTHPLTFADARVPRENLLGARGSGYANFLSILDEGRIAIAALATGAAQGCVDESVKYANQRQSFGQPIGAYQAIGFKIARMEARAHVARTAYYDAAAKMLAGKPFKKEAAIAKMISSEAAMDNSRDATQIHGGYGFMNEYPVARHYRDSKVLEIGEGTTEVQLMLIARSLGLQ