echA19 Family assigned · medium auto-curated
H37Rv Rv3516 · MTBC0 mtbc0_003732 ·
263 aa · 3976221–3977012 (+) ·
RefSeq NP_218033.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | enoyl-CoA hydratase EchA19 |
|---|---|
| MTBC0 PGAP re-annotation | crotonase/enoyl-CoA hydratase family protein |
| Revised (this work) | Crotonase/enoyl-CoA hydratase family protein. Pfam: ECH_1 (PF00378.26), ECH_2 (PF16113.11). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53561
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Enoyl-CoA hydratase EchA19 |
| EC (curated) |
EC 4.2.1.-
|
| Curated function | Degradation of the cholesterol side chain involves 3 multistep beta-oxidation cycles, this may be involved in the second cycle (Probable). Hydrates 3-OCDO-CoA ((22E)-3-oxo-chol-4,22-dien-24-oyl-CoA) to make (22R)-HOCO-CoA (3-oxo-chol-4-ene-(22R)-hydroxy-24-oyl-CoA). Also acts on octenoyl-CoA. Not active on (E)-3-OCDS-CoA ((E)-3-oxocholest-4,24-dien-26-oyl-CoA) or 3-OPDC-CoA (3-oxo-4,17-pregnadiene-20-carboxyl-CoA). Hydrates the same substrate as ChsH3, but the 2 enzymes make different stereoisomers of the product. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | echA19 |
| eggNOG description | Enoyl-CoA hydratase |
| Orthologous group | COG1024 |
| EC number |
EC 4.2.1.17
|
| KEGG orthology |
K01692
|
| KEGG pathways |
map00071, map00280, map00281, map00310, map00360, map00362, map00380, map00410, map00627, map00640, map00650, map00903, map00930, map01100, map01110, map01120, map01130, map01212
|
| KEGG modules |
M00032, M00087
|
| Gene Ontology (47) |
GO:0003674, GO:0003824, GO:0004300, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005739, GO:0006082, GO:0006629, GO:0006631, GO:0006635 +35 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 | 0.676 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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 |
|---|---|---|---|---|
ECH_1 | PF00378.26 | 2.2e-56 | 16–262 | Enoyl-CoA hydratase/isomerase |
ECH_2 | PF16113.11 | 1.3e-27 | 17–195 | Enoyl-CoA hydratase/isomerase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadD19 (acyl-CoA synthetase), high confidence from genomic context alone (score 789 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0468 fadB2 |
3-hydroxybutyryl-CoA dehydrogenase | 879 | 872 | database:650 |
Rv1867 hyp |
hypothetical protein | 863 | 856 ctx | fusion:454 database:447 |
Rv3504 fadE26 |
acyl-CoA dehydrogenase FadE26 | 894 | 850 | database:643 |
Rv1715 fadB3 |
3-hydroxybutyryl-CoA dehydrogenase FadB | 897 | 845 | database:650 |
Rv0131c fadE1 |
acyl-CoA dehydrogenase FadE1 | 852 | 845 | database:750 |
Rv0975c fadE13 |
acyl-CoA dehydrogenase FadE13 | 852 | 845 | database:750 |
Rv0154c fadE2 |
acyl-CoA dehydrogenase FadE2 | 851 | 844 | database:750 |
Rv2500c fadE19 |
acyl-CoA dehydrogenase FadE19 | 851 | 844 | database:750 |
Rv0400c fadE7 |
acyl-CoA dehydrogenase FadE7 | 851 | 844 | database:750 |
Rv3140 fadE23 |
acyl-CoA dehydrogenase FadE23 | 851 | 844 | database:750 |
Rv0231 fadE4 |
acyl-CoA dehydrogenase FadE4 | 849 | 844 | database:750 |
Rv3522 ltp4 |
lipid transfer protein | 970 | 840 | database:447 textmining:826 |
Rv3505 fadE27 |
acyl-CoA dehydrogenase FadE27 | 876 | 819 | database:643 |
Rv3523 ltp3 |
lipid carrier protein | 973 | 813 | database:447 textmining:865 |
Rv3515c fadD19 |
acyl-CoA synthetase | 964 | 789 ctx | neighborhood:607 textmining:836 |
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: enoyl-CoA hydratase EchA19
- MTBC0 PGAP product: crotonase/enoyl-CoA hydratase family protein
- Pfam (hmmscan --cut_ga): ECH_1 PF00378.26 (E=2e-56), ECH_2 PF16113.11 (E=1e-27)
- (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_218033.1)
- Domains: Pfam-A via hmmscan --cut_ga — ECH_1 (PF00378.26), ECH_2 (PF16113.11)
- 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
COG1024 - Curated reference: UniProt O53561 (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 —
163 functional partner(s); context anchor
fadD19 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003732|Rv3516|echA19 MESGPDALVERRGHTLIVTMNRPAARNALSTEMMRIMVQAWDRVDNDPDIRCCILTGAGGYFCAGMDLKAATQKPPGDSFKDGSYDPSRIDALLKGRRLTKPLIAAVEGPAIAGGTEILQGTDIRVAGESAKFGISEAKWSLYPMGGSAVRLVRQIPYTLACDLLLTGRHITAAEAKEMGLIGHVVPDGQALTKALELADAISANGPLAVQAILRSIRETECMPENEAFKIDTQIGIKVFLSDDAKEGPRAFAEKRAPNFQNR