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0  structures 222  species 0  interactions 1117  sequences 45  architectures

Family: Takusan (PF04822)

Summary: Takusan

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.

Takusan Provide feedback

This domain is named takusan, which is a Japanese word meaning 'many'. Members of this family regulate synaptic activity [1].

Literature references

  1. Tu S, Shin Y, Zago WM, States BA, Eroshkin A, Lipton SA, Tong GG, Nakanishi N;, Neuron. 2007;55:69-85.: Takusan: a large gene family that regulates synaptic activity. PUBMED:17610818 EPMC:17610818


This tab holds annotation information from the InterPro database.

InterPro entry IPR006907

This domain is found in an number of proteins, including Disks large homologue 5 and members of the takusan gene family [ PUBMED:17610818 ].

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
(32)
Full
(1117)
Representative proteomes UniProt
(1638)
RP15
(359)
RP35
(524)
RP55
(897)
RP75
(1131)
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
(32)
Full
(1117)
Representative proteomes UniProt
(1638)
RP15
(359)
RP35
(524)
RP55
(897)
RP75
(1131)
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
(32)
Full
(1117)
Representative proteomes UniProt
(1638)
RP15
(359)
RP35
(524)
RP55
(897)
RP75
(1131)
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_3835 (release 7.6)
Previous IDs: DUF622;
Type: Family
Sequence Ontology: SO:0100021
Author: Mifsud W , Eberhardt R
Number in seed: 32
Number in full: 1117
Average length of the domain: 83.4 aa
Average identity of full alignment: 44 %
Average coverage of the sequence by the domain: 6.51 %

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 28.1 28.1
Trusted cut-off 28.7 29.4
Noise cut-off 27.7 28.0
Model length: 85
Family (HMM) version: 16
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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The tree shows the occurrence of this domain across different species. 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
A0A087WQP8 View 3D Structure Click here
A0A0G2JE01 View 3D Structure Click here
A0A0G2JFD5 View 3D Structure Click here
A0A0G2JFY7 View 3D Structure Click here
A0A0G2JGJ6 View 3D Structure Click here
A0A0G2JGR8 View 3D Structure Click here
A0A0G2JU86 View 3D Structure Click here
A0A0G2JUD5 View 3D Structure Click here
A0A0G2JV71 View 3D Structure Click here
A0A0G2JY84 View 3D Structure Click here
A0A0G2JYM2 View 3D Structure Click here
A0A0G2JZD4 View 3D Structure Click here
A0A0G2K3U0 View 3D Structure Click here
A0A0G2K4J5 View 3D Structure Click here
A0A0G2K5K0 View 3D Structure Click here
A0A0G2K5W7 View 3D Structure Click here
A0A0G2K6K5 View 3D Structure Click here
A0A0G2K6X5 View 3D Structure Click here
A0A0G2K7W9 View 3D Structure Click here
A0A0G2K8M4 View 3D Structure Click here
A0A0G2K9V5 View 3D Structure Click here
A0A286YDG0 View 3D Structure Click here
A3KN63 View 3D Structure Click here
A4FTZ7 View 3D Structure Click here
A6NAS4 View 3D Structure Click here
A6NAS7 View 3D Structure Click here
A6NAT4 View 3D Structure Click here
D3YXI8 View 3D Structure Click here
D3YYI9 View 3D Structure Click here
D3Z235 View 3D Structure Click here
D3Z236 View 3D Structure Click here
D3Z257 View 3D Structure Click here
D3Z6R1 View 3D Structure Click here
D3Z7A4 View 3D Structure Click here
D3Z884 View 3D Structure Click here
D3ZJJ1 View 3D Structure Click here
D3ZJS4 View 3D Structure Click here
D3ZJU8 View 3D Structure Click here
D3ZKL6 View 3D Structure Click here
D3ZNN4 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;