Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | enoyl-CoA hydratase EchA2 |
|---|
| 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 |
O07179
TrEMBL · unreviewed
· Evidence at protein level
|
|---|
| UniProt name | Enoyl-CoA hydratase EchA2 |
|---|
| Curated function | Could possibly oxidize fatty acids using specific components. |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|
| Preferred name | echA2 |
|---|
| eggNOG description | Belongs to the enoyl-CoA hydratase isomerase family |
|---|
| 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
|
|---|
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 |
0.547 · relaxed/neutral
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
3 synonymous, 5 missense, 0 nonsense, 2 frameshift
|
|---|
| Disruption |
2 distinct premature-stop/frameshift site(s); most common in
0.65% of strains
(938) · 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 |
|---|
ECH_1 | PF00378.26 |
2.8e-28 | 16–239 |
Enoyl-CoA hydratase/isomerase |
ECH_2 | PF16113.11 |
5.9e-17 | 18–212 |
Enoyl-CoA hydratase/isomerase |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv0231 fadE4 |
acyl-CoA dehydrogenase FadE4 |
853 |
848 |
database:750 |
Rv0131c fadE1 |
acyl-CoA dehydrogenase FadE1 |
851 |
845 |
database:750 |
Rv0975c fadE13 |
acyl-CoA dehydrogenase FadE13 |
850 |
845 |
database:750 |
Rv3140 fadE23 |
acyl-CoA dehydrogenase FadE23 |
859 |
844 |
database:750 |
Rv0154c fadE2 |
acyl-CoA dehydrogenase FadE2 |
849 |
844 |
database:750 |
Rv2500c fadE19 |
acyl-CoA dehydrogenase FadE19 |
849 |
844 |
database:750 |
Rv0400c fadE7 |
acyl-CoA dehydrogenase FadE7 |
849 |
844 |
database:750 |
Rv0455c hyp |
hypothetical protein |
796 |
796 ctx |
neighborhood:795 |
Rv2524c fas |
fatty acid synthase |
816 |
789 |
coexpression:646 |
Rv1715 fadB3 |
3-hydroxybutyryl-CoA dehydrogenase FadB |
764 |
755 |
database:650 |
Rv0468 fadB2 |
3-hydroxybutyryl-CoA dehydrogenase |
763 |
754 |
database:650 |
Rv0860 fadB |
fatty oxidation protein FadB |
764 |
752 |
database:650 |
Rv1074c fadA3 |
beta-ketoacyl CoA thiolase FadA |
761 |
751 |
database:447 |
Rv0859 fadA |
acyltransferase |
760 |
751 |
database:447 |
Rv3556c fadA6 |
acetyl-CoA acetyltransferase FadA |
760 |
750 |
database:447 |
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 EchA2
- MTBC0 PGAP product: crotonase/enoyl-CoA hydratase family protein
- Pfam (hmmscan --cut_ga): ECH_1 PF00378.26 (E=3e-28), ECH_2 PF16113.11 (E=6e-17)
- (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_214970.1)
- 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
O07179
(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 —
141 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000478|Rv0456c|echA2
MPTPDFQTLLYTTAGPVATITLNRPEQLNTIVPPMPDEIEAAIGLAERDQDIKVIVLRGAGRAFSGGYDFGGGFQHWGDAMMTDGRWDPGKDFAMVTARETGPTQKFMAIWRASKPVIAQVHGWCVGGASDYALCADIVIASEDAVIGTPYSRMWGAYLTGMWLYRLSLAKVKWHSLTGRPLTGVQAAEAELINEAVPFERLEARVAEIATELARIPLSQLQAQKLIVNQAYENMGLASTQLLGGILDGLMRNTPDALEFIRTAQTQGVRAAVERRDGPFGDYSQAPPELRPDPTHVITPDGSM
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