Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
0  structures 796  species 0  interactions 1945  sequences 35  architectures

Family: Put_Phosphatase (PF06888)

Summary: Putative Phosphatase

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

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Putative Phosphatase Provide feedback

This family contains a number of putative eukaryotic acid phosphatases. Some family members represent the products of the PSI14 phosphatase family in Lycopersicon esculentum (Tomato) [1].

Literature references

  1. Baldwin JC, Karthikeyan AS, Raghothama KG; , Plant Physiol 2001;125:728-737.: Leps2, a phosphorus starvation-induced novel acid phosphatase from tomato. PUBMED:11161030 EPMC:11161030


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR016965

This group represents phosphatases related to PHOSPHO1 and PHOSPHO2 [ PUBMED:14983068 ]. It includes plant phosphatases with homology to the haloacid dehalogenase (HAD) superfamily [ PUBMED:21122813 , PUBMED:11161030 ]. PHOSPHO1 is a phosphoethanolamine/phosphocholine phosphatase [ PUBMED:15175005 ], while PHOSPHO2 has high activity toward pyridoxal 5'-phosphate (PLP), and it is active at much lower level toward pyrophosphate, phosphoethanolamine (PEA)and phosphocholine (PCho) [ PUBMED:16054448 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

Loading domain graphics...

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
(9)
Full
(1945)
Representative proteomes UniProt
(3484)
RP15
(312)
RP35
(998)
RP55
(1654)
RP75
(2173)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(9)
Full
(1945)
Representative proteomes UniProt
(3484)
RP15
(312)
RP35
(998)
RP55
(1654)
RP75
(2173)
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
(9)
Full
(1945)
Representative proteomes UniProt
(3484)
RP15
(312)
RP35
(998)
RP55
(1654)
RP75
(2173)
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: Pfam-B_7115 (release 10.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Vella Briffa B
Number in seed: 9
Number in full: 1945
Average length of the domain: 206.10 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 80.69 %

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 20.3 20.3
Trusted cut-off 20.3 20.3
Noise cut-off 20.2 20.2
Model length: 234
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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
A0A0P0V4W4 View 3D Structure Click here
A0A0R0IY18 View 3D Structure Click here
A0A1D6FYL6 View 3D Structure Click here
A0A1D6H6N1 View 3D Structure Click here
A0A1D6H6N1 View 3D Structure Click here
A0A1D6NLE4 View 3D Structure Click here
A0A1D6NLE4 View 3D Structure Click here
A4HSV3 View 3D Structure Click here
A4HSV3 View 3D Structure Click here
A9JRB9 View 3D Structure Click here
B4F825 View 3D Structure Click here
B6TXH8 View 3D Structure Click here
G3V6P4 View 3D Structure Click here
I1KGE5 View 3D Structure Click here
I1KGE6 View 3D Structure Click here
I1KPS8 View 3D Structure Click here
I1KUW1 View 3D Structure Click here
I1KUW2 View 3D Structure Click here
I1KUW3 View 3D Structure Click here
I1M5D5 View 3D Structure Click here
I1MCY1 View 3D Structure Click here
K7M3P4 View 3D Structure Click here
K7M947 View 3D Structure Click here
Q4DZE2 View 3D Structure Click here
Q4E2Y3 View 3D Structure Click here
Q66HC4 View 3D Structure Click here
Q67YC0 View 3D Structure Click here
Q6DBV4 View 3D Structure Click here
Q6H6J4 View 3D Structure Click here
Q8R2H9 View 3D Structure Click here
Q8TCD6 View 3D Structure Click here
Q8TCT1 View 3D Structure Click here
Q8W0E7 View 3D Structure Click here
Q9D9M5 View 3D Structure Click here
Q9FZ62 View 3D Structure Click here
Q9SU92 View 3D Structure Click here
Q9VWF0 View 3D Structure Click here
Q9VWF3 View 3D Structure Click here

Family Structural Model

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;