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0  structures 602  species 0  interactions 3122  sequences 122  architectures

Family: DUF1087 (PF06465)

Summary: CHD subfamily II, DUF1087

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

This is the Wikipedia entry entitled "Domain of unknown function". More...

Domain of unknown function Edit Wikipedia article

A Domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF188 and DUF1000. There are now over 3,000 DUF families within the Pfam database representing over 20% of known families.

History

The DUF naming scheme was introduced by Chris Ponting, through the addition of DUF1 and DUF2 to the SMART database.[1] These two domains were found to be widely distributed in bacterial signaling proteins. Subsequently, the functions of these domains were identified and they have since been renamed as the GGDEF domain and EAL domain respectively.

Structure

Structural genomics programmes have attempted to understand the function of DUFs through structure determination. The structures of over 250 DUF families have been solved.[2]

External Links

List of Pfam familes beginning with the letter D, including DUF families

References

  1. ^ Schultz J, Milpetz F, Bork P, Ponting CP (1998). "SMART, a simple modular architecture research tool: identification of signaling domains". Proc. Natl. Acad. Sci. U.S.A. 95 (11): 5857–64. PMC 34487. PMID 9600884. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ^ Jaroszewski L, Li Z, Krishna SS; et al. (2009). "Exploration of uncharted regions of the protein universe". PLoS Biol. 7 (9): e1000205. doi:10.1371/journal.pbio.1000205. PMC 2744874. PMID 19787035. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

"DUF" families are annotated with the Domain of unknown function Wikipedia article. This is a general article, with no specific information about individual Pfam DUFs. If you have information about this particular DUF, please let us know using the "Add annotation" button below.

CHD subfamily II, DUF1087 Provide feedback

This domain is found in chromatin remodelling factors (CHDs) from subfamily II [1] including CHD3/4/5 from animals and PICKLE. from Arabidopsis. The exact function is, as yet, unknown.

Literature references

  1. Ho KK, Zhang H, Golden BL, Ogas J;, Biochim Biophys Acta. 2013;1829:199-210.: PICKLE is a CHD subfamily II ATP-dependent chromatin remodeling factor. PUBMED:23128324 EPMC:23128324


This tab holds annotation information from the InterPro database.

InterPro entry IPR009463

This domain is found in various chromatin remodelling factors. Its function is, as yet, unknown.

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
(17)
Full
(3122)
Representative proteomes UniProt
(4380)
RP15
(307)
RP35
(929)
RP55
(2302)
RP75
(3183)
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
(17)
Full
(3122)
Representative proteomes UniProt
(4380)
RP15
(307)
RP35
(929)
RP55
(2302)
RP75
(3183)
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
(17)
Full
(3122)
Representative proteomes UniProt
(4380)
RP15
(307)
RP35
(929)
RP55
(2302)
RP75
(3183)
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: ADDA_2403
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Yeats C , Sammut SJ
Number in seed: 17
Number in full: 3122
Average length of the domain: 61.5 aa
Average identity of full alignment: 61 %
Average coverage of the sequence by the domain: 3.42 %

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 22.8 22.8
Trusted cut-off 22.8 23.2
Noise cut-off 22.7 22.7
Model length: 65
Family (HMM) version: 16
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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Tree controls

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

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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
A0A044VIM1 View 3D Structure Click here
A0A077Z2I2 View 3D Structure Click here
A0A0K0DV54 View 3D Structure Click here
A0A0K0ETI6 View 3D Structure Click here
A0A0N4UAR8 View 3D Structure Click here
A0A0R0IJ30 View 3D Structure Click here
A0A0R4IJ89 View 3D Structure Click here
A0A1D6EW42 View 3D Structure Click here
A0A1D6IBX9 View 3D Structure Click here
A0A1D6NTP5 View 3D Structure Click here
A0A1P6BYH3 View 3D Structure Click here
A0A2R8Q3B4 View 3D Structure Click here
A0A368UK75 View 3D Structure Click here
A0A3P7DBX0 View 3D Structure Click here
A0A3Q0KIA2 View 3D Structure Click here
A2A8L1 View 3D Structure Click here
B1AR17 View 3D Structure Click here
D3ZD32 View 3D Structure Click here
E9PU01 View 3D Structure Click here
F1LPP8 View 3D Structure Click here
F1QWV5 View 3D Structure Click here
F1RBT2 View 3D Structure Click here
F4JTF6 View 3D Structure Click here
F4KBP5 View 3D Structure Click here
G5EBZ4 View 3D Structure Click here
I1K8P5 View 3D Structure Click here
K7KIF9 View 3D Structure Click here
K7KPZ4 View 3D Structure Click here
O16102 View 3D Structure Click here
O97159 View 3D Structure Click here
Q12873 View 3D Structure Click here
Q14839 View 3D Structure Click here
Q22516 View 3D Structure Click here
Q6PDQ2 View 3D Structure Click here
Q8TDI0 View 3D Structure Click here
Q9S775 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;