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155  structures 8802  species 0  interactions 67281  sequences 483  architectures

Family: HAD_2 (PF13419)

Summary: Haloacid dehalogenase-like hydrolase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Haloacid dehalogenase-like hydrolase Provide feedback

No Pfam abstract.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR041492

The haloacid dehalogenase (HAD) superfamily includes a diverse range of enzymes that use an asp carboxylate as a nucleophile [ PUBMED:22607316 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan HAD (CL0137), which has the following description:

This clan represents the haloacid dehalogenase (HAD) superfamily that includes a diverse range of enzymes that use an asp carboxylate as a nucleophile [1].

The clan contains the following 25 members:

5_nucleotid Acid_phosphat_B Acid_PPase APP1_cat Cation_ATPase DHH DUF2608 DUF705 HAD HAD_2 Hydrolase Hydrolase_3 Hydrolase_6 Hydrolase_like LNS2 NIF NT5C PGP_phosphatase PhoLip_ATPase_C PMM PNK3P Put_Phosphatase S6PP Trehalose_PPase UMPH-1

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(50)
Full
(67281)
Representative proteomes UniProt
(302932)
RP15
(8439)
RP35
(31209)
RP55
(66784)
RP75
(117762)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(50)
Full
(67281)
Representative proteomes UniProt
(302932)
RP15
(8439)
RP35
(31209)
RP55
(66784)
RP75
(117762)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(50)
Full
(67281)
Representative proteomes UniProt
(302932)
RP15
(8439)
RP35
(31209)
RP55
(66784)
RP75
(117762)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download    

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Jackhmmer:B0SBQ3
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Coggill P
Number in seed: 50
Number in full: 67281
Average length of the domain: 176.10 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 70.55 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.8 23.8
Trusted cut-off 23.8 23.8
Noise cut-off 23.7 23.7
Model length: 178
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Tree controls

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the HAD_2 domain has been found. There are 155 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0N7KH54 View 3D Structure Click here
A0A0P0V8H7 View 3D Structure Click here
A0A0P0X9N9 View 3D Structure Click here
A0A0P0XXQ7 View 3D Structure Click here
A0A0R0FX63 View 3D Structure Click here
A0A0R0KYK9 View 3D Structure Click here
A0A0R0LJ61 View 3D Structure Click here
A0A1D6F343 View 3D Structure Click here
A0A1D6IM44 View 3D Structure Click here
A0A1D6JD24 View 3D Structure Click here
A0A1D6K8X3 View 3D Structure Click here
A0A1D6LTG4 View 3D Structure Click here
A0A1D6LYF1 View 3D Structure Click here
A0A1D6PSP4 View 3D Structure Click here
A0A1D8PPR2 View 3D Structure Click here
A3B7M9 View 3D Structure Click here
A3BYP4 View 3D Structure Click here
B2RYT7 View 3D Structure Click here
B4FA53 View 3D Structure Click here
B4FF48 View 3D Structure Click here
B4FI81 View 3D Structure Click here
B4FL38 View 3D Structure Click here
B4FM45 View 3D Structure Click here
B4FN43 View 3D Structure Click here
B4FTM3 View 3D Structure Click here
B4FXA2 View 3D Structure Click here
B4FZG6 View 3D Structure Click here
B4G0I2 View 3D Structure Click here
B6TFB5 View 3D Structure Click here
B6TML6 View 3D Structure Click here
B8JKD6 View 3D Structure Click here
C6T4S6 View 3D Structure Click here
C6T7T3 View 3D Structure Click here
C6TIM6 View 3D Structure Click here
D3ZEH4 View 3D Structure Click here
D7SFJ0 View 3D Structure Click here
F1RE99 View 3D Structure Click here
F4IX29 View 3D Structure Click here
F4J510 View 3D Structure Click here
F4JTE7 View 3D Structure Click here