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0  structures 912  species 0  interactions 2943  sequences 171  architectures

Family: DDT (PF02791)

Summary: DDT domain

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.

DDT domain Provide feedback

The DDT domain is named after (DNA binding homeobox and Different Transcription factors) and is approximately 60 residues in length [1]. Along with the WHIM motifs, it comprises an entirely alpha helical module found in diverse eukaryotic chromatin proteins [2]. Based on the structure of Ioc3, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins [2]. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes [2]. In particular, the DDT domain, in combination with the WHIM1 and WHIM2 motifs form the SLIDE domain binding pocket [2].

Literature references

  1. Doerks T, Copley R, Bork P; , Trends Biochem Sci 2001;26:145-146.: DDT -- a novel domain in different transcription and chromosome remodeling factors. PUBMED:11246006 EPMC:11246006

  2. Aravind L, Iyer LM;, Cell Cycle. 2012;11:119-131.: The HARE-HTH and associated domains: novel modules in the coordination of epigenetic DNA and protein modifications. PUBMED:22186017 EPMC:22186017

  3. Yamada K, Frouws TD, Angst B, Fitzgerald DJ, DeLuca C, Schimmele K, Sargent DF, Richmond TJ;, Nature. 2011;472:448-453.: Structure and mechanism of the chromatin remodelling factor ISW1a. PUBMED:21525927 EPMC:21525927


This tab holds annotation information from the InterPro database.

InterPro entry IPR018501

The DDT has been named after the better characterised DNA-binding homeobox- containing proteins and the Different Transcription and chromatin remodelling factors in which it is found. It is a domain of about 60 amino acids which is exclusively associated with nuclear domains like AT-Hook, PHD finger, methyl-CpG-binding domain, bromodomain and DNA-binding homeodomain.

The DDT domain is characterised by a number of conserved aromatic and charged residues and is predicted to consist of three alpha helices. A DNA-binding function for the DDT domain has been proposed [PUBMED:11246006].

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, 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
(182)
Full
(2943)
Representative proteomes UniProt
(4154)
NCBI
(9341)
Meta
(2)
RP15
(628)
RP35
(1398)
RP55
(2035)
RP75
(2366)
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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
(182)
Full
(2943)
Representative proteomes UniProt
(4154)
NCBI
(9341)
Meta
(2)
RP15
(628)
RP35
(1398)
RP55
(2035)
RP75
(2366)
Alignment:
Format:
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Sequence:
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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
(182)
Full
(2943)
Representative proteomes UniProt
(4154)
NCBI
(9341)
Meta
(2)
RP15
(628)
RP35
(1398)
RP55
(2035)
RP75
(2366)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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: [1]
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Iyer LM , Aravind L , Bateman A
Number in seed: 182
Number in full: 2943
Average length of the domain: 58.70 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 3.84 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.8 21.8
Trusted cut-off 21.8 21.8
Noise cut-off 21.7 21.7
Model length: 60
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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