!!

Powering down the Pfam website
On October 5th, we will start redirecting the traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro). The Pfam website will be available at pfam-legacy.xfam.org until January 2023, when it will be decommissioned. You can read more about the sunset period in our blog post.

Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
0  structures 151  species 0  interactions 1392  sequences 19  architectures

Family: Dehydrin (PF00257)

Summary: Dehydrin

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 "Dehydrin". More...

Dehydrin Edit Wikipedia article

Dehydrins are a family of proteins present in plants that are produced in response to low temperatures and drought stress. They may do this through protecting membranes from damage. [1] Their production is induced by ABA and in response to salt. Dehydrins in barley and maize are extremely hydrophilic and glycine-rich. [2] They may also play a role in allowing plants to tolerate high salt concentrations. [3]

See also

Antifreeze protein

References

  1. ^ http://www.ncbi.nlm.nih.gov/pubmed/15356392?dopt=Abstract Plant Molecular Biology 2004 Mar;54(5):743-53. Overexpression of multiple dehydrin genes enhances tolerance to freezing stress in Arabidopsis. Puhakainen T, Hess MW, Mäkelä P, Svensson J, Heino P, Palva ET.
  2. ^ http://www.ncbi.nlm.nih.gov/pubmed/2562763 Plant Molecular Biology 1989 Jul;13(1):95-108. A cDNA-based comparison of dehydration-induced proteins (dehydrins) in barley and corn. Close TJ, Kortt AA, Chandler PM.
  3. ^ http://www.ncbi.nlm.nih.gov/pubmed/16367967 A dehydrin gene in Physcomitrella patens is required for salt and osmotic stress tolerance. Plant Journal. 45(2):237-249, January 2006.Saavedra, Laura; Svensson, Jan; Carballo, Valentina;, Izmendi, Darwin; Welin, Bjorn; Vidal, Sabina.

External links

[1]

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

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.

Dehydrin Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000167

Dehydrin has been classified as part of the LEA family (D-11 from Dure, or group 2 from Bray) [ PUBMED:18318901 ]. Dehydrins contribute to freezing stress tolerance in plants and it was suggested that this could be partly due to their protective effect on membranes [ PUBMED:15356392 ].

Dehydrins share a number of structural features. One of the most notable features is the presence, in their central region, of a continuous run of five to nine serines followed by a cluster of charged residues. Such a region has been found in all known dehydrins so far with the exception of pea dehydrins. A second conserved feature is the presence of two copies of a lysine-rich octapeptide; the first copy is located just after the cluster of charged residues that follows the poly-serine region and the second copy is found at the C-terminal extremity.

LEA (late embryogenesis abundant) proteins were first identified in land plants. Plant LEA proteins have been found to accumulate to high levels during the last stage of seed formation (when a natural desiccation of the seed tissues takes place) and during periods of water deficit in vegetative organs. Later, LEA homologues have also been found in various species [ PUBMED:21034219 , PUBMED:10681550 ]. They have been classified into several subgroups in Pfam and according to Bray and Dure [ PUBMED:18318901 ].

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...

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 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
(15)
Full
(1392)
Representative proteomes UniProt
(3057)
RP15
(163)
RP35
(684)
RP55
(1167)
RP75
(1527)
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
(15)
Full
(1392)
Representative proteomes UniProt
(3057)
RP15
(163)
RP35
(684)
RP55
(1167)
RP75
(1527)
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
(15)
Full
(1392)
Representative proteomes UniProt
(3057)
RP15
(163)
RP35
(684)
RP55
(1167)
RP75
(1527)
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: Prosite & Pfam-B_3306 (Release 7.5)
Previous IDs: dehydrin;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Bateman A
Number in seed: 15
Number in full: 1392
Average length of the domain: 120.7 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 74.2 %

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 30.6 30.6
Trusted cut-off 30.6 30.6
Noise cut-off 30.3 30.5
Model length: 174
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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...

Loading sunburst data...

Tree controls

Hide

The 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.

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
A0A1D6FP59 View 3D Structure Click here
A0A1D6FP64 View 3D Structure Click here
A0A1D6FP69 View 3D Structure Click here
A0A1D6FP95 View 3D Structure Click here
A2ZDX4 View 3D Structure Click here
A2ZDX6 View 3D Structure Click here
A2ZDX8 View 3D Structure Click here
A2ZDX9 View 3D Structure Click here
A3KLI1 View 3D Structure Click here
B4FKQ0 View 3D Structure Click here
B4G1H1 View 3D Structure Click here
B6UGS5 View 3D Structure Click here
C4J477 View 3D Structure Click here
C6TAX7 View 3D Structure Click here
I1LVC1 View 3D Structure Click here
I1M0W1 View 3D Structure Click here
K7L505 View 3D Structure Click here
O23957 View 3D Structure Click here
P09442 View 3D Structure Click here
P12950 View 3D Structure Click here
P21298 View 3D Structure Click here
P22240 View 3D Structure Click here
P25863 View 3D Structure Click here
P30185 View 3D Structure Click here
P30287 View 3D Structure Click here
P31168 View 3D Structure Click here
P42758 View 3D Structure Click here
P42759 View 3D Structure Click here
P42763 View 3D Structure Click here
P46524 View 3D Structure Click here
P46525 View 3D Structure Click here
P46526 View 3D Structure Click here
Q00742 View 3D Structure Click here
Q2R4Z4 View 3D Structure Click here
Q2R4Z5 View 3D Structure Click here
Q2R4Z7 View 3D Structure Click here
Q2R4Z8 View 3D Structure Click here
Q53JR9 View 3D Structure Click here
Q6ESR4 View 3D Structure Click here
Q96261 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;