Summary: Metalloenzyme superfamily
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Metalloenzyme superfamily Provide feedback
This family includes phosphopentomutase P07651 and 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, P37689. This family is also related to PF00245 [1]. The alignment contains the most conserved residues that are probably involved in metal binding and catalysis.
Literature references
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Galperin MY, Bairoch A, Koonin EV; , Protein Sci 1998;7:1829-1835.: A superfamily of metalloenzymes unifies phosphopentomutase and cofactor- independent phosphoglycerate mutase with alkaline phosphatases and sulfatases. PUBMED:10082381 EPMC:10082381
Internal database links
SCOOP: | Alk_phosphatase DUF1501 DUF229 iPGM_N PglZ PhosphMutase Phosphodiest Sulfatase |
Similarity to PfamA using HHSearch: | Alk_phosphatase Sulfatase Phosphodiest iPGM_N PhosphMutase |
External database links
SCOP: | 1o99 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR006124
This domain unites alkaline phosphatase, N-acetylgalactosamine-4-sulphatase, and cerebroside sulphatase, enzymes with known three-dimensional structures, with phosphopentomutase, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, phosphoglycerol transferase, phosphonate monoesterase, streptomycin-6-phosphate phosphatase, alkaline phosphodiesterase/nucleotide pyrophosphatase PC-1, and several closely related sulphatases. This domain is also related to alkaline phosphatase INTERPRO [PUBMED:10082381]. The most conserved residues are probably involved in metal binding and catalysis.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | metal ion binding (GO:0046872) |
catalytic activity (GO:0003824) |
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 Alk_phosphatase (CL0088), which has the following description:
The members of this clan all share a common structure of their catalytic domains, which contain conserved metal binding residues [1].
The clan contains the following 10 members:
Alk_phosphatase DUF1501 DUF229 DUF4976 Metalloenzyme PglZ Phosphodiest Phosphoesterase Sulfatase Sulfatase_CAlignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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 (28) |
Full (9108) |
Representative proteomes | UniProt (43743) |
NCBI (73700) |
Meta (1863) |
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RP15 (1458) |
RP35 (4809) |
RP55 (8805) |
RP75 (14394) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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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 (28) |
Full (9108) |
Representative proteomes | UniProt (43743) |
NCBI (73700) |
Meta (1863) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (1458) |
RP35 (4809) |
RP55 (8805) |
RP75 (14394) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Pfam-B_1926 (release 4.1) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bateman A |
Number in seed: | 28 |
Number in full: | 9108 |
Average length of the domain: | 430.50 aa |
Average identity of full alignment: | 23 % |
Average coverage of the sequence by the domain: | 93.71 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 248 | ||||||||||||
Family (HMM) version: | 19 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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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Interactions
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 Metalloenzyme domain has been found. There are 90 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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