htdZ Resolved · high auto-curated
H37Rv Rv0130 · MTBC0 mtbc0_000141 ·
151 aa · 158193–158648 (+) ·
RefSeq NP_214644.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 3-hydroxyl-thioester dehydratase |
|---|---|
| MTBC0 PGAP re-annotation | 3-hydroxyacyl-thioester dehydratase HtdZ |
| Revised (this work) | 3-hydroxyacyl-thioester dehydratase HtdZ. Pfam: MaoC_dehydratas (PF01575.26), FAS1_DH_region (PF13452.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNP3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 3-hydroxyacyl-thioester dehydratase Z |
| EC (curated) |
EC 4.2.1.-, EC 4.2.1.119, EC 4.2.1.55
|
| Curated function | Shows trans-enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydratase activity. In vitro, can hydrate (2E)-butenoyl-CoA, (2E)-hexenoyl-CoA and (2E)-decenoyl-CoA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| eggNOG description | dehydratase |
| Orthologous group | COG2030 |
| Gene Ontology (30) |
GO:0003674, GO:0003824, GO:0004300, GO:0006082, GO:0006629, GO:0006631, GO:0006633, GO:0008150, GO:0008152, GO:0008610, GO:0009058, GO:0009987 +18 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 | 1.381 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 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 |
|---|---|---|---|---|
MaoC_dehydratas | PF01575.26 | 1.5e-34 | 11–131 | MaoC like domain |
FAS1_DH_region | PF13452.12 | 3.4e-06 | 14–128 | FAS1-like, dehydratase domain region |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadB4 (NADPH quinone oxidoreductase FadB), high confidence from genomic context alone (score 811 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3141 fadB4 |
NADPH quinone oxidoreductase FadB | 815 | 811 ctx | fusion:741 |
Rv0149 |
quinone oxidoreductase | 710 | 703 ctx | fusion:575 |
Rv3560c fadE30 |
acyl-CoA dehydrogenase FadE30 | 667 | 650 | |
Rv1934c fadE17 |
acyl-CoA dehydrogenase FadE17 | 659 | 642 | |
Rv3339c icd1 |
isocitrate dehydrogenase | 632 | 632 | database:476 |
Rv0154c fadE2 |
acyl-CoA dehydrogenase FadE2 | 629 | 610 | |
Rv3562 fadE31 |
acyl-CoA dehydrogenase FadE31 | 615 | 598 | |
Rv3564 fadE33 |
acyl-CoA dehydrogenase FadE33 | 597 | 577 | |
Rv3573c fadE34 |
acyl-CoA dehydrogenase FadE34 | 591 | 570 | |
Rv0271c fadE6 |
acyl-CoA dehydrogenase FadE6 | 587 | 566 | |
Rv0148 |
short-chain type dehydrogenase/reductase | 583 | 565 | |
Rv0860 fadB |
fatty oxidation protein FadB | 588 | 562 | |
Rv3761c fadE36 |
acyl-CoA dehydrogenase FadE36 | 572 | 556 | |
Rv0125 pepA |
serine protease PepA | 551 | 552 | database:498 |
Rv1043c hyp |
hypothetical protein | 550 | 550 | database:498 |
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: 3-hydroxyl-thioester dehydratase
- MTBC0 PGAP product: 3-hydroxyacyl-thioester dehydratase HtdZ
- Pfam (hmmscan --cut_ga): MaoC_dehydratas PF01575.26 (E=1e-34), FAS1_DH_region PF13452.12 (E=3e-06)
- (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_214644.1)
- Domains: Pfam-A via hmmscan --cut_ga — MaoC_dehydratas (PF01575.26), FAS1_DH_region (PF13452.12)
- 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
COG2030 - Curated reference: UniProt P9WNP3 (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 —
126 functional partner(s); context anchor
fadB4 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000141|Rv0130|htdZ MRTFESVADLAAAAGEKVGQSDWVTITQEEVNLFADATGDHQWIHVDPERAAAGPFGTTIAHGFMTLALLPRLQHQMYTVKGVKLAINYGLNKVRFPAPVPVGSRVRATSSLVGVEDLGNGTVQATVSTTVEVEGSAKPACVAESIVRYVA