Summary: Zein-binding
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.
Zein-binding Provide feedback
This domain binds to zein proteins, PF01559 [1]. Zein proteins are seed storage proteins.
Literature references
-
Holding DR, Otegui MS, Li B, Meeley RB, Dam T, Hunter BG, Jung R, Larkins BA;, Plant Cell. 2007;19:2569-2582.: The maize floury1 gene encodes a novel endoplasmic reticulum protein involved in zein protein body formation. PUBMED:17693529 EPMC:17693529
This tab holds annotation information from the InterPro database.
InterPro entry IPR007656
The GTD-binding domain is a plant-specific protein-protein interaction domain. It emerged in primitive land plants and founded a multigene family that is conserved in all flowering plants. Proteins with GTD-binding domains fall into four groups, where group 1-3 contain the GTD-binding domain at the C-terminal half of the protein and one (group 2) or more (group1) predicted transmembrane domains, or an endoplasmic reticulum signal peptide (group 3) at the N- terminus, whereas group 4 contains the GTD-binding domain near the N terminus. GTD-binding domain proteins may constitute a family of myosin receptors, which are associated with the surface of specific plant organelles, bind to the globular tail domain (GTD) of myosin motor proteins, and thereby promote actin-dependent organelle motility. It seems likely that myosin binding is a common property of the GTD-binding domain, whereas the ability of FLOURY1 to bind maize-specific zeins is a specific feature of this endoplasmic reticulum (ER)-associated protein.
The GTD-binding domain is predicted to adopt a coiled-coil structure.
Some proteins known to contain a GTD-binding domain are listed below:
- Maize FLOURY1 (FL1), which belongs to group 1. Its GTD-binding domain facilitates the localization of 22kDa alpha-zein [PUBMED:17693529].
- Arabidopsis myosin binding (MyoB) proteins 1-6 and 7, which belong respectively to group 3 and 4. They bind to myosin XI [PUBMED:23995081].
- Tobacco RAC5 interacting subapical pollen tube protein (RISAP), which belongs to group 3. It binds via its GTD-binding domain to the GTD domain of a pollen tube myosin XI [PUBMED:25387880].
- Lily LLP13, which belongs to group 3. It is likely a cytoskeleton-binding protein that binds with intermediate filaments (IFs) that potentially exist in pollen tubes [PUBMED:24944111].
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
Loading domain graphics...
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 (64) |
Full (1848) |
Representative proteomes | UniProt (2595) |
NCBI (3756) |
Meta (0) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (81) |
RP35 (918) |
RP55 (1501) |
RP75 (1875) |
||||||
Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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 (64) |
Full (1848) |
Representative proteomes | UniProt (2595) |
NCBI (3756) |
Meta (0) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (81) |
RP35 (918) |
RP55 (1501) |
RP75 (1875) |
||||||
Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Pfam-B_2802 (release 7.5) |
Previous IDs: | DUF593; |
Type: | Coiled-coil |
Sequence Ontology: | SO:0001080 |
Author: |
Mifsud W |
Number in seed: | 64 |
Number in full: | 1848 |
Average length of the domain: | 90.00 aa |
Average identity of full alignment: | 46 % |
Average coverage of the sequence by the domain: | 14.88 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
Model details: |
|
||||||||||||
Model length: | 92 | ||||||||||||
Family (HMM) version: | 16 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
Selections
Align selected sequences to HMM
Generate a FASTA-format file
Clear selection
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...
Tree controls
HideThe tree shows the occurrence of this domain across different species. More...
Loading...
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.