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8  structures 253  species 0  interactions 1240  sequences 27  architectures

Family: Ded_cyto (PF06920)

Summary: Dedicator of cytokinesis

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This is the Wikipedia entry entitled "DOCK (protein)". More...

DOCK (protein) Edit Wikipedia article

Dedicator of cytokinesis
Identifiers
Symbol Ded_cyto
Pfam PF06920
InterPro IPR010703
SCOP 1wg7
SUPERFAMILY 1wg7

DOCK (Dedicator of cytokinesis) is a family of related proteins involved in intracellular signalling networks.[1] Studies to date suggest that this family act as guanine nucleotide exchange factors for small G proteins of the Rho family, such as Rac and Cdc42. DOCK family proteins are categorised into four subfamilies based on their sequence homology:

  • DOCK-A subfamily
  • DOCK-B subfamily
  • DOCK-C subfamily (also known as Zir subfamily)
    • Dock6 (also known as Zir1)
    • Dock7 (also known as Zir2)
    • Dock8 (also known as Zir3)
  • DOCK-D subfamily (also known as Zizimin subfamily)
    • Dock9 (also known as Zizimin1)
    • Dock10 (also known as Zizimin3)
    • Dock11 (also known as Zizimin2)

References[edit]

  1. ^ Côté JF, Vuori K (December 2002). "Identification of an evolutionarily conserved superfamily of DOCK180-related proteins with guanine nucleotide exchange activity". J. Cell. Sci. 115 (Pt 24): 4901–13. doi:10.1242/jcs.00219. PMID 12432077. 


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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.

Dedicator of cytokinesis Provide feedback

This family represents a conserved region approximately 200 residues long within a number of eukaryotic dedicator of cytokinesis proteins. These are potential guanine nucleotide exchange factors, which activate some small GTPases by exchanging bound GDP for free GTP.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010703

This family represents a conserved region of approximately 200 residues within a number of eukaryotic dedicator of cytokinesis (DOCK) proteins. These proteins are potential guanine nucleotide exchange factors that activate some small GTPases, such as Rac, by exchanging bound GDP for free GTP [PUBMED:12432077]. DOCK proteins are required during several cellular processes, such as cell motility and phagocytosis. For instance, DOCK2 is specifically expressed in haemopoietic cells, and plays a critical role in lymphocyte migration [PUBMED:12829596].

Gene Ontology

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Domain organisation

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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(25)
Full
(1240)
Representative proteomes NCBI
(1086)
Meta
(2)
RP15
(199)
RP35
(276)
RP55
(456)
RP75
(667)
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Format an alignment

  Seed
(25)
Full
(1240)
Representative proteomes NCBI
(1086)
Meta
(2)
RP15
(199)
RP35
(276)
RP55
(456)
RP75
(667)
Alignment:
Format:
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Sequence:
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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
(25)
Full
(1240)
Representative proteomes NCBI
(1086)
Meta
(2)
RP15
(199)
RP35
(276)
RP55
(456)
RP75
(667)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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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_7154 (release 10.0)
Previous IDs: none
Type: Family
Author: Vella Briffa B
Number in seed: 25
Number in full: 1240
Average length of the domain: 172.80 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 10.33 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.6 20.6
Trusted cut-off 20.6 20.8
Noise cut-off 20.5 20.5
Model length: 178
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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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 Ded_cyto domain has been found. There are 8 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 seqence.

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