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0  structures 885  species 0  interactions 11828  sequences 422  architectures

Family: DDE_1 (PF03184)

Summary: DDE superfamily endonuclease

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.

DDE superfamily endonuclease Provide feedback

This family of proteins are related to PF00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localised to the centromere.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004875

Proteins containing this domain are probably endonucleases of the DDE superfamily. This domain contains three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Proteins containing this domain include tigger transposable element derived proteins from mammals [ PUBMED:15487591 ] and protein Pdc2 from budding yeasts [ PUBMED:22404710 ]. Interestingly, proteins conatining this domain also includes the Centromere Protein B (CENP-B) protein, which appears to have lost the metal binding residues in this domain and is unlikely to have endonuclease activity. CENP-B is a an inner kinetochore protein that binds to a specific centromere sequence [ PUBMED:18072184 ].

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...

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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
(12)
Full
(11828)
Representative proteomes UniProt
(21257)
RP15
(3963)
RP35
(7249)
RP55
(10699)
RP75
(13300)
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
(12)
Full
(11828)
Representative proteomes UniProt
(21257)
RP15
(3963)
RP35
(7249)
RP55
(10699)
RP75
(13300)
Alignment:
Format:
Order:
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
(12)
Full
(11828)
Representative proteomes UniProt
(21257)
RP15
(3963)
RP35
(7249)
RP55
(10699)
RP75
(13300)
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_2254 (release 6.5)
Previous IDs: CENP-B; DDE;
Type: Family
Sequence Ontology: SO:0100021
Author: Mifsud W , Bateman A
Number in seed: 12
Number in full: 11828
Average length of the domain: 144.00 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 31.05 %

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 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.9
Model length: 175
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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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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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
A0A0G2JY58 View 3D Structure Click here
A0A0G2KAW9 View 3D Structure Click here
A0A0G2KDY1 View 3D Structure Click here
A0A0G2KPX7 View 3D Structure Click here
A0A0G2L218 View 3D Structure Click here
A0A0R0G3K6 View 3D Structure Click here
A0A0R4IN51 View 3D Structure Click here
A0A1D8PER5 View 3D Structure Click here
A0A1D8PSB5 View 3D Structure Click here
A0A1D8PTV2 View 3D Structure Click here
A7YY82 View 3D Structure Click here
B1WC39 View 3D Structure Click here
B2RRL2 View 3D Structure Click here
D3ZS21 View 3D Structure Click here
D3ZV46 View 3D Structure Click here
D4AC64 View 3D Structure Click here
F1LVC4 View 3D Structure Click here
M0R5M5 View 3D Structure Click here
O14423 View 3D Structure Click here
O60108 View 3D Structure Click here
O75564 View 3D Structure Click here
P07199 View 3D Structure Click here
P27790 View 3D Structure Click here
P32896 View 3D Structure Click here
P49777 View 3D Structure Click here
Q0VBL1 View 3D Structure Click here
Q17RP2 View 3D Structure Click here
Q499M4 View 3D Structure Click here
Q4W5G0 View 3D Structure Click here
Q53EQ6 View 3D Structure Click here
Q5AL59 View 3D Structure Click here
Q60976 View 3D Structure Click here
Q6B0B8 View 3D Structure Click here
Q6NT04 View 3D Structure Click here
Q7TM95 View 3D Structure Click here
Q7Z3K3 View 3D Structure Click here
Q80TC5 View 3D Structure Click here
Q8BUZ3 View 3D Structure Click here
Q8BZH4 View 3D Structure Click here
Q8IY51 View 3D Structure Click here

trRosetta Structure

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;