echA20 Family assigned · medium auto-curated
H37Rv Rv3550 · MTBC0 mtbc0_003767 ·
247 aa · 4012830–4013573 (+) ·
RefSeq NP_218067.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | enoyl-CoA hydratase EchA20 |
|---|---|
| MTBC0 PGAP re-annotation | enoyl-CoA hydratase family protein |
| Revised (this work) | 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 |
I6Y3U6
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | (7aS)-7a-methyl-1,5-dioxo-2,3,5,6,7,7a-hexahydro-1H-indene-carboxyl-CoA hydrolase |
| EC (curated) |
EC 4.1.99.-
|
| Curated function | Involved in the final steps of cholesterol and steroid degradation. Catalyzes the hydrolytic ring D opening of (7aS)-7a-methyl-1,5-dioxo-2,3,5,6,7,7a-hexahydro-1H-indene-carboxyl-CoA (HIEC-CoA) to (3E)-2-(2-carboxylatoethyl)-3-methyl-6-oxocyclohex-1-ene-1-carboxyl-CoA (COCHEA-CoA) (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | echA20 |
| 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
|
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 | 0.351 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 | 1.3e-36 | 10–209 | Enoyl-CoA hydratase/isomerase |
ECH_2 | PF16113.11 | 3.0e-20 | 22–198 | Enoyl-CoA hydratase/isomerase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3551 (CoA-transferase subunit alpha), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3551 |
CoA-transferase subunit alpha | 999 | 998 ctx | neighborhood:882 cooccurence:746 coexpression:869 database:500 textmining:634 |
Rv3552 |
CoA-transferase subunit beta | 999 | 998 ctx | neighborhood:882 cooccurence:749 coexpression:869 database:500 textmining:564 |
Rv3549c |
short-chain type dehydrogenase/reductase | 995 | 985 ctx | neighborhood:787 cooccurence:422 coexpression:849 textmining:698 |
Rv3553 |
oxidoreductase | 988 | 979 ctx | neighborhood:773 coexpression:864 textmining:472 |
Rv3548c |
short-chain type dehydrogenase/reductase | 983 | 968 ctx | neighborhood:716 coexpression:785 textmining:498 |
Rv3560c fadE30 |
acyl-CoA dehydrogenase FadE30 | 993 | 938 ctx | cooccurence:497 coexpression:811 textmining:896 |
Rv3522 ltp4 |
lipid transfer protein | 928 | 909 ctx | cooccurence:649 database:447 |
Rv3559c |
oxidoreductase | 942 | 894 ctx | cooccurence:561 database:591 textmining:478 |
Rv3562 fadE31 |
acyl-CoA dehydrogenase FadE31 | 962 | 892 ctx | cooccurence:641 coexpression:538 textmining:667 |
Rv3561 fadD3 |
fatty-acid--CoA ligase FadD3 | 977 | 883 | coexpression:841 textmining:818 |
Rv3523 ltp3 |
lipid carrier protein | 913 | 879 ctx | cooccurence:536 database:447 |
Rv3540c ltp2 |
lipid transfer protein | 907 | 877 ctx | cooccurence:526 database:447 |
Rv3541c chsH1 hyp |
hypothetical protein | 854 | 848 ctx | cooccurence:721 |
Rv3140 fadE23 |
acyl-CoA dehydrogenase FadE23 | 851 | 845 | database:750 |
Rv2500c fadE19 |
acyl-CoA dehydrogenase FadE19 | 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: enoyl-CoA hydratase EchA20
- MTBC0 PGAP product: enoyl-CoA hydratase family protein
- Pfam (hmmscan --cut_ga): ECH_1 PF00378.26 (E=1e-36), ECH_2 PF16113.11 (E=3e-20)
- (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_218067.1)
- 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 I6Y3U6 (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 —
166 functional partner(s); context anchor
Rv3551 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003767|Rv3550|echA20 MPITSTTPEPGIVAVTVDYPPVNAIPSKAWFDLADAVTAAGANSDTRAVILRAEGRGFNAGVDIKEMQRTEGFTALIDANRGCFAAFRAVYECAVPVIAAVNGFCVGGGIGLVGNSDVIVASEDATFGLPEVERGALGAATHLSRLVPQHLMRRLFFTAATVDAATLQHFGSVHEVVSRDQLDEAALRVARDIAAKDTRVIRAAKEALNFIDVQRVNASYRMEQGFTFELNLAGVADEHRDAFVKKS