dhaA Resolved · high auto-curated
H37Rv Rv2579 · MTBC0 - ·
300 aa · 2903639–2904541 (+) ·
RefSeq YP_177890.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | haloalkane dehalogenase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Haloalkane dehalogenase. Pfam: Abhydrolase_1 (PF00561.27), Abhydrolase_6 (PF12697.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WMR9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Haloalkane dehalogenase 3 |
| EC (curated) |
EC 3.8.1.5
|
| Curated function | Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | dhaA |
| eggNOG description | Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons |
| Orthologous group | COG0596 |
| EC number |
EC 3.8.1.5
|
| KEGG orthology |
K01563
|
| KEGG pathways |
map00361, map00625, map01100, map01120
|
| Gene Ontology (32) |
GO:0003674, GO:0003824, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006805, GO:0008150, GO:0008152, GO:0009056, GO:0009410, GO:0009987 +20 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 | 0.616 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 6 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.72% of strains (1048) · 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 |
|---|---|---|---|---|
Abhydrolase_1 | PF00561.27 | 2.6e-19 | 32–279 | alpha/beta hydrolase fold |
Abhydrolase_6 | PF12697.14 | 6.7e-12 | 33–283 | Alpha/beta hydrolase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lipZ (hydrolase), medium confidence from genomic context alone (score 573 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1833c dhmA2 |
haloalkane dehalogenase | 930 | 928 | database:900 |
Rv2296 dhmA1 |
haloalkane dehalogenase | 926 | 927 | database:900 |
Rv0162c adhE1 |
zinc-type alcohol dehydrogenase subunit E | 912 | 913 | database:900 |
Rv0761c adhB |
alcohol dehydrogenase B | 912 | 912 | database:900 |
Rv1862 adhA |
alcohol dehydrogenase A | 903 | 904 | database:900 |
Rv1530 adh |
alcohol dehydrogenase | 906 | 902 | database:900 |
Rv2578c hyp |
hypothetical protein | 598 | 599 ctx | neighborhood:593 |
Rv1834 lipZ |
hydrolase | 572 | 573 ctx | cooccurence:570 |
Rv2627c hyp |
hypothetical protein | 520 | 503 | |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 527 | 500 | experimental:441 |
Rv1527c pks5 |
polyketide synthase | 617 | 498 | experimental:441 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 526 | 498 | experimental:441 |
Rv2048c pks12 |
polyketide synthase | 526 | 498 | experimental:441 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 526 | 498 | experimental:441 |
Rv1124 ephC |
epoxide hydrolase EphC | 482 | 482 ctx | cooccurence:479 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): haloalkane dehalogenase
- Pfam (hmmscan --cut_ga): Abhydrolase_1 PF00561.27 (E=3e-19), Abhydrolase_6 PF12697.14 (E=7e-12)
- (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 YP_177890.1)
- Domains: Pfam-A via hmmscan --cut_ga — Abhydrolase_1 (PF00561.27), Abhydrolase_6 (PF12697.14)
- 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
COG0596 - Curated reference: UniProt P9WMR9 (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 —
23 functional partner(s); context anchor
lipZ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2579|dhaA MTAFGVEPYGQPKYLEIAGKRMAYIDEGKGDAIVFQHGNPTSSYLWRNIMPHLEGLGRLVACDLIGMGASDKLSPSGPDRYSYGEQRDFLFALWDALDLGDHVVLVLHDWGSALGFDWANQHRDRVQGIAFMEAIVTPMTWADWPPAVRGVFQGFRSPQGEPMALEHNIFVERVLPGAILRQLSDEEMNHYRRPFVNGGEDRRPTLSWPRNLPIDGEPAEVVALVNEYRSWLEETDMPKLFINAEPGAIITGRIRDYVRSWPNQTEITVPGVHFVQEDSPEEIGAAIAQFVRRLRSAAGV