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155  structures 1566  species 0  interactions 11580  sequences 164  architectures

Family: GED (PF02212)

Summary: Dynamin GTPase effector 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.

Dynamin GTPase effector domain Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003130

This entry represents the dynamin GTPase effector domain (GED) found in proteins related to dynamin. Its C-terminal region constitutes one of the helices of the bundle signalling element (BSE) or neck together with the N- and C-terminal regions from the Gtpase domain, being in close proximity and functionally linked to it. The N-terminal region of GED is part of the stalk domain [ PUBMED:22233676 ].

Dynamin is a GTP-hydrolysing protein that is an essential participant in clathrin-mediated endocytosis by cells. It self-assembles into 'collars' in vivo at the necks of invaginated coated pits; the self-assembly of dynamin being coordinated by the GTPase domain. Mutation studies indicate that dynamin functions as a molecular regulator of receptor-mediated endocytosis [ PUBMED:22233676 , PUBMED:10206643 ].

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
(72)
Full
(11580)
Representative proteomes UniProt
(17411)
RP15
(1623)
RP35
(4418)
RP55
(8761)
RP75
(11959)
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
(72)
Full
(11580)
Representative proteomes UniProt
(17411)
RP15
(1623)
RP35
(4418)
RP55
(8761)
RP75
(11959)
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
(72)
Full
(11580)
Representative proteomes UniProt
(17411)
RP15
(1623)
RP35
(4418)
RP55
(8761)
RP75
(11959)
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: Alignment kindly provided by SMART
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: SMART
Number in seed: 72
Number in full: 11580
Average length of the domain: 90.5 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 12.55 %

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 21.4 21.4
Trusted cut-off 21.4 21.4
Noise cut-off 21.3 21.3
Model length: 92
Family (HMM) version: 21
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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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the GED domain has been found. There are 155 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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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
A0A044S959 View 3D Structure Click here
A0A044T7Y0 View 3D Structure Click here
A0A077YYG1 View 3D Structure Click here
A0A077ZA59 View 3D Structure Click here
A0A0D2DPM1 View 3D Structure Click here
A0A0D2G173 View 3D Structure Click here
A0A0K0E066 View 3D Structure Click here
A0A0K0EMI2 View 3D Structure Click here
A0A0K0ESX8 View 3D Structure Click here
A0A0N4UIU4 View 3D Structure Click here
A0A0P0W699 View 3D Structure Click here
A0A0P0W9A2 View 3D Structure Click here
A0A0R0FD34 View 3D Structure Click here
A0A0R0FKB4 View 3D Structure Click here
A0A0R0H0V0 View 3D Structure Click here
A0A0R0IKS3 View 3D Structure Click here
A0A0R4IBZ4 View 3D Structure Click here
A0A0R4IIR1 View 3D Structure Click here
A0A158Q5C1 View 3D Structure Click here
A0A175VUR8 View 3D Structure Click here
A0A175W8B4 View 3D Structure Click here
A0A1C1CHQ3 View 3D Structure Click here
A0A1C1CV34 View 3D Structure Click here
A0A1D6ECY4 View 3D Structure Click here
A0A1D6ELQ4 View 3D Structure Click here
A0A1D6FJS7 View 3D Structure Click here
A0A1D6G5W0 View 3D Structure Click here
A0A1D6HJQ5 View 3D Structure Click here
A0A1D6JWT6 View 3D Structure Click here
A0A1D6K8W1 View 3D Structure Click here
A0A1D6MC12 View 3D Structure Click here
A0A1D6N309 View 3D Structure Click here
A0A1D6NRA8 View 3D Structure Click here
A0A1D6Q9Y4 View 3D Structure Click here
A0A1D8PKC9 View 3D Structure Click here
A0A1D8PN45 View 3D Structure Click here
A0A3P7E1T7 View 3D Structure Click here
A0A3P7FXC0 View 3D Structure Click here
A0A3Q0KF72 View 3D Structure Click here
A0A3Q0KLH5 View 3D Structure Click here