echA9 Family assigned · medium auto-curated
H37Rv Rv1071c · MTBC0 mtbc0_001151 ·
345 aa · 1203324–1204361 (-) ·
RefSeq NP_215587.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | enoyl-CoA hydratase EchA9 |
|---|---|
| MTBC0 PGAP re-annotation | enoyl-CoA hydratase/isomerase family protein |
| Revised (this work) | Enoyl-CoA hydratase/isomerase 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 |
O53419
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 3-hydroxyisobutyryl-CoA hydrolase |
| EC (curated) |
EC 3.1.2.4
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | echA9 |
| 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 | 0.431 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 5 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 | 7.7e-29 | 13–194 | Enoyl-CoA hydratase/isomerase |
ECH_2 | PF16113.11 | 2.9e-120 | 16–336 | Enoyl-CoA hydratase/isomerase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: echA8 (enoyl-CoA hydratase EchA8), high confidence from genomic context alone (score 973 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1070c echA8 |
enoyl-CoA hydratase EchA8 | 974 | 973 ctx | neighborhood:876 coexpression:731 |
Rv0751c mmsB |
3-hydroxyisobutyrate dehydrogenase | 965 | 963 ctx | fusion:898 cooccurence:474 |
Rv1069c hyp |
hypothetical protein | 879 | 880 ctx | neighborhood:876 |
Rv0400c fadE7 |
acyl-CoA dehydrogenase FadE7 | 870 | 866 | database:750 |
Rv3140 fadE23 |
acyl-CoA dehydrogenase FadE23 | 853 | 845 | database:750 |
Rv0231 fadE4 |
acyl-CoA dehydrogenase FadE4 | 850 | 845 | database:750 |
Rv0154c fadE2 |
acyl-CoA dehydrogenase FadE2 | 850 | 845 | database:750 |
Rv0131c fadE1 |
acyl-CoA dehydrogenase FadE1 | 850 | 845 | database:750 |
Rv0975c fadE13 |
acyl-CoA dehydrogenase FadE13 | 850 | 845 | database:750 |
Rv2500c fadE19 |
acyl-CoA dehydrogenase FadE19 | 849 | 844 | database:750 |
Rv0860 fadB |
fatty oxidation protein FadB | 802 | 790 | database:650 |
Rv2524c fas |
fatty acid synthase | 815 | 788 | coexpression:644 |
Rv3563 fadE32 |
acyl-CoA dehydrogenase FadE32 | 952 | 778 | database:643 textmining:794 |
Rv2502c accD1 |
acetyl-/propionyl-CoA carboxylase subunit beta | 772 | 761 | database:650 |
Rv0468 fadB2 |
3-hydroxybutyryl-CoA dehydrogenase | 769 | 760 | database:650 |
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 EchA9
- MTBC0 PGAP product: enoyl-CoA hydratase/isomerase family protein
- Pfam (hmmscan --cut_ga): ECH_1 PF00378.26 (E=8e-29), ECH_2 PF16113.11 (E=3e-120)
- (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_215587.1)
- 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 O53419 (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 —
145 functional partner(s); context anchor
echA8 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001151|Rv1071c|echA9 MTGESHEVLTNVEGGVGFVTLNRPKAINSLNQTMVDLLATVLMSWEHEDAVHAVVLSGAGERGLCAGGDVVAVYHSARKDGVEARRFWRHEYLLNALIGRFAKPYVALMDGIVMGGGVGVSAHANTRVVTDTSKVAMPEVGIGFIPDVGGVYLLSRAPGALGLHAALTGAPFSGADAIALGFADHFVPHGDLDAFTQKIVTGGVESALAAHAVEPPPSTLAAQRDWIDECYAGDSVADIVAALRKQGGEPAVNASDLIASRSPIALSVTLQAVRRAAKLDTLEDVLIQDYRVSSASLRSHDLVEGIRAQLIDKDRNPNWSPATLDAITAADIEAYFEPVDDDLSF