Rv1833c Resolved · high auto-curated
H37Rv Rv1833c · MTBC0 mtbc0_001946 ·
286 aa · 2096961–2097821 (-) ·
RefSeq NP_216349.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | haloalkane dehalogenase |
|---|---|
| MTBC0 PGAP re-annotation | haloalkane dehalogenase |
| Revised (this work) | Haloalkane dehalogenase. Pfam: Abhydrolase_1 (PF00561.27), Abhydrolase_6 (PF12697.14), Hydrolase_4 (PF12146.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMS1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Haloalkane dehalogenase 2 |
| 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 | dhmA |
| eggNOG description | Haloalkane dehalogenase |
| Orthologous group | COG0596 |
| EC number |
EC 3.8.1.5
|
| KEGG orthology |
K01563
|
| KEGG pathways |
map00361, map00625, map01100, map01120
|
| Gene Ontology (7) |
GO:0005575, GO:0005576, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.976 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 |
|---|---|---|---|---|
Abhydrolase_1 | PF00561.27 | 1.2e-29 | 35–274 | alpha/beta hydrolase fold |
Abhydrolase_6 | PF12697.14 | 1.8e-16 | 37–280 | Alpha/beta hydrolase family |
Hydrolase_4 | PF12146.16 | 2.9e-08 | 37–245 | Serine aminopeptidase, S33 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lipZ (hydrolase), medium confidence from genomic context alone (score 667 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2579 dhaA |
haloalkane dehalogenase | 930 | 928 | database:900 |
Rv2296 dhmA1 |
haloalkane dehalogenase | 925 | 925 | database:900 |
Rv0162c adhE1 |
zinc-type alcohol dehydrogenase subunit E | 912 | 912 | database:900 |
Rv0761c adhB |
alcohol dehydrogenase B | 912 | 912 | database:900 |
Rv1862 adhA |
alcohol dehydrogenase A | 904 | 904 | database:900 |
Rv1530 adh |
alcohol dehydrogenase | 906 | 903 | database:900 |
Rv1834 lipZ |
hydrolase | 667 | 667 ctx | neighborhood:575 |
Rv1938 ephB |
epoxide hydrolase EphB | 560 | 561 ctx | cooccurence:558 |
Rv1836c hyp |
hypothetical protein | 555 | 556 ctx | neighborhood:544 |
Rv3171c hpx |
non-heme haloperoxidase Hpx | 515 | 516 ctx | cooccurence:514 |
Rv3670 ephE |
epoxide hydrolase EphE | 513 | 513 ctx | cooccurence:513 |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 529 | 501 | experimental:441 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 529 | 501 | experimental:441 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 527 | 500 | experimental:441 |
Rv1527c pks5 |
polyketide synthase | 526 | 498 | experimental:441 |
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: haloalkane dehalogenase
- MTBC0 PGAP product: haloalkane dehalogenase
- Pfam (hmmscan --cut_ga): Abhydrolase_1 PF00561.27 (E=1e-29), Abhydrolase_6 PF12697.14 (E=2e-16), Hydrolase_4 PF12146.16 (E=3e-08)
- (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_216349.1)
- Domains: Pfam-A via hmmscan --cut_ga — Abhydrolase_1 (PF00561.27), Abhydrolase_6 (PF12697.14), Hydrolase_4 (PF12146.16)
- 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 P9WMS1 (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 —
51 functional partner(s); context anchor
lipZ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001946|Rv1833c| MSIDFTPDPQLYPFESRWFDSSRGRIHYVDEGTGPPILLCHGNPTWSFLYRDIIVALRDRFRCVAPDYLGFGLSERPSGFGYQIDEHARVIGEFVDHLGLDRYLSMGQDWGGPISMAVAVERADRVRGVVLGNTWFWPADTLAMKAFSRVMSSPPVQYAILRRNFFVERLIPAGTEHRPSSAVMAHYRAVQPNAAARRGVAEMPKQILAARPLLARLAREVPATLGTKPTLLIWGMKDVAFRPKTIIPRLSATFPDHVLVELPNAKHFIQEDAPDRIAAAIIERFG