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109  structures 140  species 0  interactions 1748  sequences 11  architectures

Family: Gamma-thionin (PF00304)

Summary: Gamma-thionin 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 "Gamma thionin". More...

Gamma thionin Edit Wikipedia article

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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.

Gamma-thionin family Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Knottin_1 (CL0054), which has the following description:

This clan includes a number of toxin families that share the knottin structure. These families come from scorpions, plants and arthropods.

The clan contains the following 15 members:

BmKX Defensin_2 Defensin_5 Defensin_like Gamma-thionin Macin SCRL SLR1-BP Toxin_17 Toxin_2 Toxin_3 Toxin_37 Toxin_38 Toxin_5 Toxin_6

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
(23)
Full
(1748)
Representative proteomes UniProt
(2868)
RP15
(136)
RP35
(857)
RP55
(1433)
RP75
(1917)
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
(23)
Full
(1748)
Representative proteomes UniProt
(2868)
RP15
(136)
RP35
(857)
RP55
(1433)
RP75
(1917)
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
(23)
Full
(1748)
Representative proteomes UniProt
(2868)
RP15
(136)
RP35
(857)
RP55
(1433)
RP75
(1917)
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
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 23
Number in full: 1748
Average length of the domain: 47.70 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 53.18 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.1 25.1
Trusted cut-off 25.1 25.1
Noise cut-off 25.0 25.0
Model length: 47
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

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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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Tree controls

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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 Gamma-thionin domain has been found. There are 109 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
A0A0P0VFC4 View 3D Structure Click here
A0A0P0W773 View 3D Structure Click here
A0A1D6EET4 View 3D Structure Click here
A0A1D6H4M3 View 3D Structure Click here
A0A1D6K7Q8 View 3D Structure Click here
A0A1D6K7Q9 View 3D Structure Click here
A0A1D6MAC5 View 3D Structure Click here
A0A1D6N294 View 3D Structure Click here
A6XER2 View 3D Structure Click here
B6SJ49 View 3D Structure Click here
B6SJS8 View 3D Structure Click here
B6SL97 View 3D Structure Click here
B6SMX5 View 3D Structure Click here
B6SQK6 View 3D Structure Click here
B6SXF2 View 3D Structure Click here
B6T249 View 3D Structure Click here
B6UHE2 View 3D Structure Click here
C5JA66 View 3D Structure Click here
C6TFR9 View 3D Structure Click here
C7IX29 View 3D Structure Click here
I1K554 View 3D Structure Click here
I1M396 View 3D Structure Click here
K7KLB4 View 3D Structure Click here
K7KVC7 View 3D Structure Click here
K7L494 View 3D Structure Click here
K7L751 View 3D Structure Click here
K7L949 View 3D Structure Click here
K7MGG1 View 3D Structure Click here
K7MPK0 View 3D Structure Click here
K7TQS7 View 3D Structure Click here
O80994 View 3D Structure Click here
O80995 View 3D Structure Click here
P30224 View 3D Structure Click here
P41964 View 3D Structure Click here
P81008 View 3D Structure Click here
P81009 View 3D Structure Click here
P82781 View 3D Structure Click here
P82782 View 3D Structure Click here
P82784 View 3D Structure Click here
P82785 View 3D Structure Click here
P82787 View 3D Structure Click here
Q07502 View 3D Structure Click here
Q0JEX4 View 3D Structure Click here
Q39182 View 3D Structure Click here
Q41914 View 3D Structure Click here
Q6H6Z3 View 3D Structure Click here
Q6H836 View 3D Structure Click here
Q6K209 View 3D Structure Click here
Q7F8K7 View 3D Structure Click here
Q7XUA9 View 3D Structure Click here
Q7YXH9 View 3D Structure Click here
Q8IRD6 View 3D Structure Click here
Q8IRD7 View 3D Structure Click here
Q9C947 View 3D Structure Click here
Q9FFP8 View 3D Structure Click here
Q9FI22 View 3D Structure Click here
Q9FI23 View 3D Structure Click here
Q9FZ31 View 3D Structure Click here
Q9VZQ4 View 3D Structure Click here
Q9VZQ5 View 3D Structure Click here
Q9VZR2 View 3D Structure Click here
Q9ZUL7 View 3D Structure Click here
Q9ZUL8 View 3D Structure Click here