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60  structures 5300  species 0  interactions 12664  sequences 129  architectures

Family: Hydrolase_6 (PF13344)

Summary: Haloacid dehalogenase-like hydrolase

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Haloacid dehalogenase-like hydrolase Provide feedback

This family is part of the HAD superfamily.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006357

These sequences form one of the structural subclasses of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs [ PUBMED:7966317 ]. The classes are defined [ PUBMED:11601995 ] based on the location and the observed or predicted fold of a so-called "capping domain" [ PUBMED:10956028 ], or the absence of such a domain. Class I consists of sequences in which the capping domain is found in between the first and second catalytic motifs. Class II consists of sequences in which the capping domain is found between the second and third motifs. Class III sequences have no capping domain in either of these positions. The Class IIA capping domain is predicted to consist of a mixed alpha-beta fold with the basic pattern: Helix-Helix-Helix-Sheet-Helix-Loop-Sheet-Helix-Sheet-Helix. Presently, this subfamily covers the eukaryotic phosphoglycolate phosphatase, as well as four further subfamilies covering closely related sequences in eukaryotes, in Gram-positive bacteria and in Gram-negative bacteria. The Escherichia coli NagD gene and the Bacillus subtilis AraL gene are members of this subfamily but are not members of the any of the presently defined equivalogs within it. NagD is part of the NAG operon responsible for N-acetylglucosamine metabolism [ PUBMED:2190615 ]. Genes from several organisms have been annotated as NagD, or NagD-like. However, without data on the presence of other members of this pathway, (such as in the case of Yersinia pestis) these assignments should not be given great weight. The AraL gene is similar and is part of the L-arabinose operon [ PUBMED:9084180 ]. A gene from Halobacterium has been annotated as AraL, but no other Ara operon genes have been annotated. Many of the genes in this subfamily have been annotated as "pNPPase" "4-nitrophenyl phosphatase" or "NPPase". These all refer to the same activity versus a common lab test compound used to determine phosphatase activity. There is no evidence that this activity is physiologically relevant. Dihydroxyacetone phosphatase from Corynebacterium glutamicum is also a member of this superfamily, and catalyzes the dephosphorylation of dihydroxyacetone phosphate to produce 1,3-dihydroxyacetone [ PUBMED:23108048 ].

The structure of NagD from Escherichia coli> (strain K12) has been reported and its activity against various substrates determined. It has high specificity for nucleotide monophosphates, and in particular UMP and GMP. In the context of its occurrence in the NAG operon, it may well be involved in the recycling of cell wall metabolites [ PUBMED:16430214 ].

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 24 members:

5_nucleotid Acid_phosphat_B Acid_PPase 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
(122)
Full
(12664)
Representative proteomes UniProt
(38528)
RP15
(1886)
RP35
(5869)
RP55
(11564)
RP75
(17984)
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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
(122)
Full
(12664)
Representative proteomes UniProt
(38528)
RP15
(1886)
RP35
(5869)
RP55
(11564)
RP75
(17984)
Alignment:
Format:
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Sequence:
Gaps:
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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
(122)
Full
(12664)
Representative proteomes UniProt
(38528)
RP15
(1886)
RP35
(5869)
RP55
(11564)
RP75
(17984)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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:Q7P3Y5
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 122
Number in full: 12664
Average length of the domain: 103.00 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 31.89 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 101
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
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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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 Hydrolase_6 domain has been found. There are 60 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
A0A0P0Y9D9 View 3D Structure Click here
A0A0R0G8D0 View 3D Structure Click here
A0A0R0GXI8 View 3D Structure Click here
A0A0R0JEK8 View 3D Structure Click here
A0A0R4IJ50 View 3D Structure Click here
A0A1D6J965 View 3D Structure Click here
A0A1D6PD31 View 3D Structure Click here
A0A1D8PDH0 View 3D Structure Click here
A0A1D8PIG2 View 3D Structure Click here
A0A1D8PNE5 View 3D Structure Click here
A4I739 View 3D Structure Click here
A4I740 View 3D Structure Click here
A4IBX2 View 3D Structure Click here
A5PLK2 View 3D Structure Click here
A6NDG6 View 3D Structure Click here
B3DI21 View 3D Structure Click here
B4F880 View 3D Structure Click here
B6TMM7 View 3D Structure Click here
D3ZDK7 View 3D Structure Click here
D3ZQB6 View 3D Structure Click here
F1QGU0 View 3D Structure Click here
I1JF10 View 3D Structure Click here
I1L677 View 3D Structure Click here
K7LBA1 View 3D Structure Click here
K7MUH9 View 3D Structure Click here
M9PJJ5 View 3D Structure Click here
O13899 View 3D Structure Click here
O16247 View 3D Structure Click here
O44538 View 3D Structure Click here
P0AF24 View 3D Structure Click here
P0DKC3 View 3D Structure Click here
P0DKC4 View 3D Structure Click here
P34492 View 3D Structure Click here
P36151 View 3D Structure Click here
P60487 View 3D Structure Click here
Q2FZX0 View 3D Structure Click here
Q3UGR5 View 3D Structure Click here
Q4CTQ5 View 3D Structure Click here
Q4D3X0 View 3D Structure Click here
Q4DAN9 View 3D Structure Click here
Q4DT94 View 3D Structure Click here
Q54P82 View 3D Structure Click here
Q54QC3 View 3D Structure Click here
Q59SK0 View 3D Structure Click here
Q59WC5 View 3D Structure Click here
Q5BJJ5 View 3D Structure Click here
Q5I0D5 View 3D Structure Click here
Q6AYR6 View 3D Structure Click here
Q6DBI9 View 3D Structure Click here
Q6EP66 View 3D Structure Click here
Q6P0Z8 View 3D Structure Click here
Q6ZJG4 View 3D Structure Click here
Q7X7H3 View 3D Structure Click here
Q8CHP8 View 3D Structure Click here
Q8GWU0 View 3D Structure Click here
Q8GZY3 View 3D Structure Click here
Q8IBV0 View 3D Structure Click here
Q8SXC0 View 3D Structure Click here
Q8SXC9 View 3D Structure Click here
Q8VD52 View 3D Structure Click here
Q91WM2 View 3D Structure Click here
Q96GD0 View 3D Structure Click here
Q9BXW7 View 3D Structure Click here
Q9D7I5 View 3D Structure Click here
Q9H008 View 3D Structure Click here
Q9H0R4 View 3D Structure Click here
Q9M169 View 3D Structure Click here
Q9TYQ4 View 3D Structure Click here
Q9VLM9 View 3D Structure Click here
Q9VVL5 View 3D Structure Click here
Q9VYT0 View 3D Structure Click here
Q9VZW4 View 3D Structure Click here
Q9W272 View 3D Structure Click here
Q9W4W5 View 3D Structure Click here