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3  structures 44  species 0  interactions 56  sequences 6  architectures

Family: AUDH_Cupin (PF18637)

Summary: Aldos-2-ulose dehydratase/isomerase (AUDH) Cupin domain

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This is the Wikipedia entry entitled "Cupin superfamily". More...

Cupin superfamily Edit Wikipedia article

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Aldos-2-ulose dehydratase/isomerase (AUDH) Cupin domain Provide feedback

The enzyme aldos-2-ulose dehydratase/isomerase (AUDH) participates in carbohydrate secondary metabolism, catalyzing the conversion of glucosone and 1,5-d-anhydrofructose to the secondary metabolites cortalcerone and microthecin, respectively. Crystal structure analysis revealed that the enzyme subunit is built up of three domains, an N-terminal seven-bladed propeller, a bicupin and a C-terminal lectin domain. This entry describes the second Cupin domain (residues 574-739) composed of two antiparallel sheets that build up the jellyroll sandwich fold formed from four and five beta-strands. This cupin domain in AUDH is found to contain a zinc binding site where the metal site is located at the bottom of the cleft formed by the beta-sandwich, as observed in many cupins [1].

Literature references

  1. Claesson M, Lindqvist Y, Madrid S, Sandalova T, Fiskesund R, Yu S, Schneider G;, J Mol Biol. 2012;417:279-293.: Crystal structure of bifunctional aldos-2-ulose dehydratase/isomerase from Phanerochaete chrysosporium with the reaction intermediate ascopyrone M. PUBMED:22330145 EPMC:22330145


This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

Domain organisation

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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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(19)
Full
(56)
Representative proteomes UniProt
(69)
NCBI
(73)
Meta
(0)
RP15
(19)
RP35
(36)
RP55
(48)
RP75
(55)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(19)
Full
(56)
Representative proteomes UniProt
(69)
NCBI
(73)
Meta
(0)
RP15
(19)
RP35
(36)
RP55
(48)
RP75
(55)
Alignment:
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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
(19)
Full
(56)
Representative proteomes UniProt
(69)
NCBI
(73)
Meta
(0)
RP15
(19)
RP35
(36)
RP55
(48)
RP75
(55)
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.

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.

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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

This family is new in this Pfam release.

Seed source: ECOD:EUF07668
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: El-Gebali S
Number in seed: 19
Number in full: 56
Average length of the domain: 139.90 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 22.55 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 33.6 25.3
Noise cut-off 23.8 23.4
Model length: 158
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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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 AUDH_Cupin domain has been found. There are 3 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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