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.
2  structures 58  species 0  interactions 153  sequences 6  architectures

Family: Barwin (PF00967)

Summary: Barwin family

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 "Barwin domain". More...

Barwin domain Edit Wikipedia article

Barwin
PDB 1bw4 EBI.jpg
three-dimensional structure in solution of barwin, a protein from barley seed
Identifiers
Symbol Barwin
Pfam PF00967
Pfam clan CL0199
InterPro IPR001153
PROSITE PDOC00619
SCOP 1bw3
SUPERFAMILY 1bw3

In molecular biology, the barwin domain is a protein domain found in barwin, a basic protein isolated from aqueous extracts of barley seeds. Barwin is 125 amino acids in length, and contains six cysteine residues that combine to form three disulphide bridges.[1][2] Comparative analysis shows the sequence of barwin to be highly similar to a 122 amino acid stretch in the C-terminal of the products of two wound-induced genes (win1 and win2) from potato, the product of the hevein gene of rubber trees, and pathogenesis-related protein 4 from tobacco. The high levels of similarity to these proteins, and their ability to bind saccharides, suggest that the barwin domain may be involved in a common defence mechanism in plants.

References[edit]

  1. ^ Svensson B, Svendsen I, Hojrup P, Roepstorff P, Ludvigsen S, Poulsen FM (September 1992). "Primary structure of barwin: a barley seed protein closely related to the C-terminal domain of proteins encoded by wound-induced plant genes". Biochemistry 31 (37): 8767–70. doi:10.1021/bi00152a012. PMID 1390663. 
  2. ^ Ludvigsen S, Poulsen FM (September 1992). "Secondary structure in solution of barwin from barley seed using 1H nuclear magnetic resonance spectroscopy". Biochemistry 31 (37): 8771–82. doi:10.1021/bi00152a013. PMID 1390664. 

This article incorporates text from the public domain Pfam and InterPro IPR001153

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.

Barwin family Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001153

Barwin is a basic protein isolated from aqueous extracts of barley seeds. It is 125 amino acids in length, and contains six cysteine residues that combine to form three disulphide bridges [PUBMED:1390663, PUBMED:1390664]. Comparative analysis shows the sequence to be highly similar to a 122 amino acid stretch in the C-terminal of the products of two wound-induced genes (win1 and win2) from potato, the product of the hevein gene of rubber trees, and pathogenesis-related protein 4 from tobacco. The high levels of similarity to these proteins, and their ability to bind saccharides, suggest that the barwin domain may be involved in a common defence mechanism in plants.

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...

Pfam Clan

This family is a member of clan DPBB (CL0199), which has the following description:

The DPBB fold is often an enzymatic domain. The members of this family are quite diverse, and if catalytic this family may contain several different functions [1,2]. This clan represents the barwin like barrels.

The clan contains the following 5 members:

3D Barwin Cerato-platanin DPBB_1 Glyco_hydro_45

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...

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
(8)
Full
(153)
Representative proteomes NCBI
(226)
Meta
(1)
RP15
(6)
RP35
(28)
RP55
(38)
RP75
(47)
Jalview View  View  View  View  View  View  View  View 
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(8)
Full
(153)
Representative proteomes NCBI
(226)
Meta
(1)
RP15
(6)
RP35
(28)
RP55
(38)
RP75
(47)
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
(8)
Full
(153)
Representative proteomes NCBI
(226)
Meta
(1)
RP15
(6)
RP35
(28)
RP55
(38)
RP75
(47)
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.

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: Sarah Teichmann
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 8
Number in full: 153
Average length of the domain: 108.50 aa
Average identity of full alignment: 60 %
Average coverage of the sequence by the domain: 69.81 %

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 20.7 20.7
Trusted cut-off 20.7 20.7
Noise cut-off 20.6 20.6
Model length: 119
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

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.

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 Barwin domain has been found. There are 2 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.

Loading structure mapping...