Top Level Name

  ⌊ Superfamily (core) Haloacid Dehalogenase

Family known
Total 100% <100% Family unknown
Functional domains 79778 21323 1224 57231
UniProtKB 394605 91661 1870 301074
GI 725118 171718 3317 550083
Structures 721
Reactions 20
Functional domains of this superfamily were last updated on June 28, 2017
New functional domains were last added to this superfamily on Aug. 1, 2014

Enzymes in the haloacid dehalogenase superfamily are related by their ability to form covalent enzyme-substrate intermediates via a conserved active site aspartic acid, thus facilitating cleavage of C-Cl, P-C, or P-O bonds. The majority of enzymes in the superfamily, including all characterized phosphotransferases, require a divalent metal ion cofactor for activity. Notable exceptions are the haloacid dehalogenases. Most superfamily members have a cap domain, with a variable fold and function. All structurally characterized superfamily members share a conserved alpha/beta-core domain, termed the "HAD-like" fold by SCOP.

Koonin, E.V. and R.L. Tatusov

Computer analysis of bacterial haloacid dehalogenases defines a large superfamily of hydrolases with diverse specificity. Application of an iterative approach to database search

▸ Abstract

J Mol Biol 1994;244(1):125-132 | PubMed ID: 7966317

Morais, M.C., et al.

The crystal structure of bacillus cereus phosphonoacetaldehyde hydrolase: insight into catalysis of phosphorus bond cleavage and catalytic diversification within the HAD enzyme superfamily

▸ Abstract

Biochemistry 2000;39(34):10385-10396 | PubMed ID: 10956028

Zhang G, Morais MC, Dai J, Zhang W, Dunaway-Mariano D, Allen KN

Investigation of metal ion binding in phosphonoacetaldehyde hydrolase identifies sequence markers for metal-activated enzymes of the HAD enzyme superfamily

▸ Abstract

Biochemistry 2004;43(17):4990-4997 | PubMed ID: 15109258

Allen KN, Dunaway-Mariano D

Phosphoryl group transfer: evolution of a catalytic scaffold

▸ Abstract

Trends Biochem Sci 2004;29(9):495-503 | PubMed ID: 15337123

EFI

Sequence Similarity Networks

Download a Sequence Similarity Network of this superfamily (XGMML format ).

Network downloads are XGMML files that are readable by program such as Cytoscape. In these networks, nodes represent proteins and edges represent pairwise similarities better than a given edge-score cutoff. The edge score is either a bit score for full networks or mean E values for a Repnet. Additionally, these networks contain several attributes with data from the SFLD.

No edge data is available for this network. Contact an SFLD curator to request this network.

List of files included in the download. A detailed list of included node attributes, their definitions, and their uses [revised: 1/24/2014].

Reaction Network

Download Reaction Network of this superfamily (XGMML format ).

Reaction Network downloads are XGMML files that are readable by program such as Cytoscape. In these networks, nodes represent proteins and edges represent pairwise similarities better than a given bitscore-cutoff. Additionally, these networks contain several attributes with data from the SFLD.

Only 8 of 20 Reactions for the Superfamily could be computed.

Reaction Network: 20-Dec-2016

Molecular Networks

Download Molecular Networks of this superfamily (XGMML format ).

Molecular Network downloads are XGMML files that are readable by program such as Cytoscape. In these networks, nodes represent molecules in a reaction and edges represent pairwise similarities better than a given bitscore-cutoff. Additionally, these networks contain several attributes with data from the SFLD.

Molecular Network: Superfamily (23-Jan-2017) Molecular Network: Superfamily substrate (23-Jan-2017) Molecular Network: Superfamily product (23-Jan-2017)

Disclaimer
Although the download speed has improved please keep in mind that network files can be quite large. We are currently working on improving the network download and finding ways to make large networks manageable. Please see How to increase memory for Cytoscape.

Multiple Sequence Alignment

View the alignment of a representative set of sequences of this superfamily using

Multiple Sequence Alignment

Align one or multiple sequences to the alignment of a representative set of sequences of this superfamily.
Enter FASTA formatted sequence(s) : and view results using

Downloads

Data Type All (#) Known (#) Unknown (#)
Full length FASTA (79778) (22547) (57231)
Complete annotation (.tsv) (79778) (22547) (57231)
Annotation suitable for Excel ® (.tsv) (79778) (22547) (57231)
Clear form

Some of these files can be quite large, please be patient during the download.

To identify your sequence later, please make sure to provide a header line starting with '>' for each sequence. Empty headers are allowed, but a header line is always required.
Cutoff Value
The least significant edge-score at which pairwise similarities are included in the network. A bit score for the full network, or a mean E value for the Repnet.
XGMML format
Open in Cytoscape via:
 Menu
 →Import
 →Network (multiple file types)
Download the annotation of all sequences as shown in the table below as a ͟Tab ͟Separated ͟Value (TSV) file. This file can be imported into a spreadsheet application.
Full length FASTA
Full length sequences in FASTA format.
Functional Domain FASTA
Sequences of the Functional Domain in FASTA format.
Complete annotation
Download complete annotation of sequences sets of this superfamily as a ͟Tab ͟Separated ͟Value (TSV) file. This file has all data but cell size can exceed the maximum supported by spreadsheet programs (such as Microsoft Excel ®).
Spreadsheet ready annotation
Annotation of sequences sets of this superfamily in a ͟Tab ͟Separated ͟Value (TSV) file. This file can be imported into a spreadsheet application. Cells which exceed the allowed spreadsheet maximum (32.5K) are preceded by the word "Truncated" and clipped short.
Total number of functional domains in this group.
Number of Functional Domains that have been manually or automatically been assigned to a family.
Number of Functional Domains that have not been assigned to a family.
Number of structures available from the PDB for members of this group.
Number of Functional Domains with 100% of Conserved Residues
Number of Functional Domains with less than 100% Conserved Residues
Subgroup ▸ Legend T K C U S
C0.1: RNA Pol CTD Phosphatase Like 1606 0 0 1606 18
C1.1: Acid Phosphatase Like 589 0 0 589 13
C1.2: Nucleotidase Like 355 1 0 354 23
┗ 1: C1.2.1 125 1 0 124 22
┗ 5'-nucleotidase 1 1 0 20
┗ 1: C1.2.2 230 0 0 230 1
C1.3: Acid Phosphatase Like 150 0 0 150 15
C1.4: 5'-Nucleotidase Like 139 0 0 139 15
C1.5: HAD, Beta-PGM, Phosphatase Like 22320 814 785 21506 272
┗ 1: C1.5.1: Epoxide Hydrolase Phosphatase Like 1561 7 7 1554 102
┗ epoxide hydrolase n-terminal phosphatase 7 7 7 27
┗ 1: C1.5.2: MDP Like 321 2 2 319 4
┗ mdp-1 2 2 2 2
┗ 1: C1.5.3: 5'-Nucleotidase Like 630 0 0 630 15
┗ 1: C1.5.4: Enolase-phosphatase Like 614 249 244 365 3
┗ enolase-phosphatase 249 249 244 3
┗ 1: C1.5.5: Heptose Bisphosphate Phosphatase Like 1994 3 3 1991 24
┗ histidinol-phosphatase 3 3 3 0
┗ 1: C1.5.6: HAD, Beta-PGM, Phosphatase Like 16453 553 529 15900 116
┗ 2-deoxyglucose-6-phosphatase 7 7 7 0
┗ 2-haloacid dehalogenase 147 147 145 12
┗ beta-phosphoglucomutase 176 176 160 21
┗ glycerol-3-phosphate phosphatase 5 5 5 1
┗ phosphoglycolate phosphatase 75 75 72 0
┗ phosphonoacetaldehyde hydrolase 143 143 140 8
C1.6: Phosphoserine Phosphatase Like 5522 1569 1545 3953 57
┗ 1: C1.6.1: Phosphoserine Phosphatase Like 3237 1404 1381 1833 23
┗ phosphoserine phosphatase 1404 1404 1381 13
┗ 1: C1.6.2: Deoxy-d-mannose-octulosonate 8-phosphate Phosphatase Like 1396 165 164 1231 30
┗ deoxy-d-mannose-octulosonate 8-phosphate phosphatase 165 165 164 13
C1.7: P-type atpase like 25354 19755 18593 5599 135
┗ p-type atpase 19755 19755 18593 99
C1.8: polynucleotide 5'-hydroxyl-kinase c-terminal phosphatase like 58 1 0 57 5
┗ polynucleotide 5'-hydroxyl-kinase c-terminal phosphatase 1 1 0 5
C2.A: Pyridoxal Phosphate Phosphatase Like 3453 68 67 3385 35
┗ phosphoglycolate phosphatase 2 67 67 67 0
┗ pyridoxal phosphatase 1 1 0 6
C2.B: Phosphomannomutase and Phosphatase Like 11460 339 333 11121 66
┗ trehalose-phosphatase 3 3 3 0
┗ 1: C2.B.1: Sucrose Phosphatase Like 609 75 70 534 10
┗ sucrose-phosphatase 75 75 70 9
┗ 1: C2.B.2: Mannosyl-3-phosphoglycerate Phosphatase Like 399 8 8 391 12
┗ mannosyl-3-phosphoglycerate phosphatase 8 8 8 11
┗ 1: C2.B.3: Phosphomannomutase Like 363 225 224 138 8
┗ alpha-phosphomannomutase 225 225 224 7
┗ 1: C2.B.4: PGP Like 7943 28 28 7915 29
┗ phosphoglycolate phosphatase 3 28 28 28 2
Depth of the multi-level Subgroup hierarchy.