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297  structures 1537  species 0  interactions 16200  sequences 166  architectures

Family: Cupin_1 (PF00190)

Summary: Cupin

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 "Cupin superfamily". More...

Cupin superfamily Edit Wikipedia article

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.

Cupin Provide feedback

This family represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant.

Literature references

  1. Dunwell JM; , Biotechnol Genet Eng Rev 1998;15:1-32.: Cupins: a new superfamily of functionally diverse proteins that include germins and plant storage proteins. PUBMED:9573603 EPMC:9573603


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006045

This entry represents the conserved beta-barrel fold of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant [ PUBMED:9573603 ].

This domain can also be found as a central component of many microbial proteins including certain types of phosphomannose isomerase, polyketide synthase, epimerase, and dioxygenase [ PUBMED:10704478 ].

Domain organisation

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

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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 (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
(63)
Full
(16200)
Representative proteomes UniProt
(30632)
RP15
(1602)
RP35
(8231)
RP55
(13195)
RP75
(18782)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(63)
Full
(16200)
Representative proteomes UniProt
(30632)
RP15
(1602)
RP35
(8231)
RP55
(13195)
RP75
(18782)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(63)
Full
(16200)
Representative proteomes UniProt
(30632)
RP15
(1602)
RP35
(8231)
RP55
(13195)
RP75
(18782)
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: Seedstore_11s;Cupin;
Type: Domain
Sequence Ontology: SO:0000417
Author: Griffiths-Jones SR
Number in seed: 63
Number in full: 16200
Average length of the domain: 139.00 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 61.07 %

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 20.4 20.4
Trusted cut-off 20.4 20.4
Noise cut-off 20.3 20.3
Model length: 151
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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Selections

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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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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 Cupin_1 domain has been found. There are 297 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
A0A0P0V8F8 View 3D Structure Click here
A0A0P0VIM4 View 3D Structure Click here
A0A0P0VUB4 View 3D Structure Click here
A0A0P0W8K1 View 3D Structure Click here
A0A0R0EA46 View 3D Structure Click here
A0A0R0EIG9 View 3D Structure Click here
A0A0R0FWA1 View 3D Structure Click here
A0A0R0FXI5 View 3D Structure Click here
A0A0R0G3Z6 View 3D Structure Click here
A0A0R0G3Z6 View 3D Structure Click here
A0A0R0G550 View 3D Structure Click here
A0A0R0GMQ0 View 3D Structure Click here
A0A0R0GMV1 View 3D Structure Click here
A0A0R0GMV1 View 3D Structure Click here
A0A0R0GUX4 View 3D Structure Click here
A0A0R0H2H7 View 3D Structure Click here
A0A0R0HYM3 View 3D Structure Click here
A0A0R0HYM3 View 3D Structure Click here
A0A0R0I0F2 View 3D Structure Click here
A0A0R0IZ14 View 3D Structure Click here
A0A0R0IZ51 View 3D Structure Click here
A0A0R0KI49 View 3D Structure Click here
A0A0R0KSG4 View 3D Structure Click here
A0A0R0L0M3 View 3D Structure Click here
A0A0R0L748 View 3D Structure Click here
A0A1D6DPN9 View 3D Structure Click here
A0A1D6DZA4 View 3D Structure Click here
A0A1D6EBM4 View 3D Structure Click here
A0A1D6EBM4 View 3D Structure Click here
A0A1D6ELU8 View 3D Structure Click here
A0A1D6H1F2 View 3D Structure Click here
A0A1D6H9X6 View 3D Structure Click here
A0A1D6HTL7 View 3D Structure Click here
A0A1D6J4J1 View 3D Structure Click here
A0A1D6JQE7 View 3D Structure Click here
A0A1D6K268 View 3D Structure Click here
A0A1D6K268 View 3D Structure Click here
A0A1D6KN97 View 3D Structure Click here
A0A1D6KN98 View 3D Structure Click here
A0A1D6L886 View 3D Structure Click here
A0A1D6M3P4 View 3D Structure Click here
A0A1D6MTQ6 View 3D Structure Click here
A0A1D6MTQ6 View 3D Structure Click here
A0A1D6N137 View 3D Structure Click here
A0A1D6N137 View 3D Structure Click here
A0A1D6NEI1 View 3D Structure Click here
A0A1D6PIB3 View 3D Structure Click here
A0A1D6PUN9 View 3D Structure Click here
A0A1D6PUP3 View 3D Structure Click here
A0A1D6PUP6 View 3D Structure Click here
A0A1D6PUQ1 View 3D Structure Click here
A0A1D6Q1Q1 View 3D Structure Click here
A0A1D6QI94 View 3D Structure Click here
A0A1X7YDQ9 View 3D Structure Click here
A0A1X7YDV3 View 3D Structure Click here
A0A1X7YDW0 View 3D Structure Click here
A1YQH2 View 3D Structure Click here
B4FAV5 View 3D Structure Click here
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B4FY73 View 3D Structure Click here
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B6UEL1 View 3D Structure Click here
C0PGM3 View 3D Structure Click here
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F1LVA4 View 3D Structure Click here
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F4KCZ4 View 3D Structure Click here
F7J077 View 3D Structure Click here
I1JCD6 View 3D Structure Click here
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I1N811 View 3D Structure Click here
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P0DO15 View 3D Structure Click here
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P11827 View 3D Structure Click here
P11827 View 3D Structure Click here
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P15455 View 3D Structure Click here
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P94040 View 3D Structure Click here
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Q02897 View 3D Structure Click here
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Q04672 View 3D Structure Click here
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Q09151 View 3D Structure Click here
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Q0DS36 View 3D Structure Click here
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Q10BU2 View 3D Structure Click here
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Q58174 View 3D Structure Click here
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Q84TL6 View 3D Structure Click here
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