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0  structures 1105  species 0  interactions 1675  sequences 5  architectures

Family: Cupin_6 (PF12852)

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

Cupin_1
PDB 1l3j EBI.jpg
crystal structure of oxalate decarboxylase formate complex
Identifiers
Symbol Cupin_1
Pfam PF00190
Pfam clan CL0029
InterPro IPR006045
SCOP 2phl
SUPERFAMILY 2phl
Cupin_2
PDB 1y3t EBI.jpg
crystal structure of yxag, a dioxygenase from bacillus subtilis
Identifiers
Symbol Cupin_2
Pfam PF07883
Pfam clan CL0029
InterPro IPR013096
SCOP 1vj2
SUPERFAMILY 1vj2
Cupin_3
PDB 1rc6 EBI.jpg
crystal structure of protein ylba from e. coli, pfam duf861
Identifiers
Symbol Cupin_3
Pfam PF05899
Pfam clan CL0029
InterPro IPR008579
SCOP 1o5u
SUPERFAMILY 1o5u
Cupin_4
Identifiers
Symbol Cupin_4
Pfam PF08007
Pfam clan CL0029
Cupin_5
PDB 1yud EBI.jpg
x-ray crystal structure of protein so0799 from shewanella oneidensis. northeast structural genomics consortium target sor12.
Identifiers
Symbol Cupin_5
Pfam PF06172
Pfam clan CL0029
InterPro IPR009327
Cupin_6
Identifiers
Symbol Cupin_6
Pfam PF12852
Pfam clan CL0029
Cupin_7
Identifiers
Symbol Cupin_7
Pfam PF12973
Pfam clan CL0029

In molecular biology, the cupin superfamily of proteins is a diverse superfamily of proteins containing a conserved barrel domain, cupa is the Latin term for a small barrel. The cupin superfamily includes a wide variety of enzymes, but notably contains the non-enzymatic seed storage proteins also.[1][2]

[edit] References

  1. ^ Dunwell JM (1998). "Cupins: a new superfamily of functionally diverse proteins that include germins and plant storage proteins". Biotechnol. Genet. Eng. Rev. 15: 1–32. PMID 9573603. 
  2. ^ Dunwell, J. M.; Purvis, A.; Khuri, S. (2004). "Cupins: The most functionally diverse protein superfamily?". Phytochemistry 65 (1): 7–17. doi:10.1016/j.phytochem.2003.08.016. PMID 14697267.  edit

This article incorporates text from the public domain Pfam and InterPro IPR013096

This article incorporates text from the public domain Pfam and InterPro IPR006045

This article incorporates text from the public domain Pfam and InterPro IPR009327

This article incorporates text from the public domain Pfam and InterPro IPR008579

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 is a family of bacterial and eukaryotic proteins that belong to the Cupin superfamily. Some of the proteins in this family are annotated as being members of the AraC family of transcription factors, in which case this domain corresponds to the ligand binding domain.

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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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
(212)
Full
(1675)
Representative proteomes NCBI
(1685)
Meta
(112)
RP15
(123)
RP35
(263)
RP55
(390)
RP75
(494)
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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
(212)
Full
(1675)
Representative proteomes NCBI
(1685)
Meta
(112)
RP15
(123)
RP35
(263)
RP55
(390)
RP75
(494)
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
(212)
Full
(1675)
Representative proteomes NCBI
(1685)
Meta
(112)
RP15
(123)
RP35
(263)
RP55
(390)
RP75
(494)
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.

Pfam alignments:

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: Pfam-B_918 (release 24.0)
Previous IDs: none
Type: Domain
Author: Mistry J
Number in seed: 212
Number in full: 1675
Average length of the domain: 171.80 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 57.25 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.5 24.5
Trusted cut-off 24.5 24.5
Noise cut-off 24.4 24.4
Model length: 186
Family (HMM) version: 2
Download: download the raw HMM for this family

Species distribution

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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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