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307  structures 8854  species 0  interactions 52255  sequences 271  architectures

Family: Transket_pyr (PF02779)

Summary: Transketolase, pyrimidine binding domain

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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.

Transketolase, pyrimidine binding domain Provide feedback

This family includes transketolase enzymes, pyruvate dehydrogenases, and branched chain alpha-keto acid decarboxylases.

Literature references

  1. Nikkola M, Lindqvist Y, Schneider G; , J Mol Biol 1994;238:387-404.: Refined structure of transketolase from Saccharomyces cerevisiae at 2.0 A resolution. PUBMED:8176731 EPMC:8176731

  2. Lindqvist Y, Schneider G, Ermler U, Sundstrom M; , EMBO J 1992;11:2373-2379.: Three-dimensional structure of transketolase, a thiamine diphosphate dependent enzyme, at 2.5 A resolution. PUBMED:1628611 EPMC:1628611

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005475

Transketolase EC (TK) catalyzes the reversible transfer of a two-carbon ketol unit from xylulose 5-phosphate to an aldose receptor, such as ribose 5-phosphate, to form sedoheptulose 7-phosphate and glyceraldehyde 3- phosphate. This enzyme, together with transaldolase, provides a link between the glycolytic and pentose-phosphate pathways. TK requires thiamine pyrophosphate as a cofactor. In most sources where TK has been purified, it is a homodimer of approximately 70 Kd subunits. TK sequences from a variety of eukaryotic and prokaryotic sources [ PUBMED:1567394 , PUBMED:1737042 ] show that the enzyme has been evolutionarily conserved. In the peroxisomes of methylotrophic yeast Pichia angusta (Yeast) (Hansenula polymorpha), there is a highly related enzyme, dihydroxy-acetone synthase (DHAS) EC (also known as formaldehyde transketolase), which exhibits a very unusual specificity by including formaldehyde amongst its substrates.

1-deoxyxylulose-5-phosphate synthase (DXP synthase) [ PUBMED:9371765 ] is an enzyme so far found in bacteria (gene dxs) and plants (gene CLA1) which catalyzes the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D- xylulose-5-phosphate (dxp), a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6). DXP synthase is evolutionary related to TK. The N-terminal section, contains a histidine residue which appears to function in proton transfer during catalysis [ PUBMED:1628611 ]. In the central section there are conserved acidic residues that are part of the active cleft and may participate in substrate-binding [ PUBMED:1628611 ]. This family includes transketolase enzymes EC and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit SWISSPROT EC . Both these enzymes utilise thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis.

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 THDP-binding (CL0254), which has the following description:

This clan includes pyruvate dehydrogenases, branched chain alpha-keto acid decarboxylases, phosphoketolases and the pyrimidine binding region of transketolases.

The clan contains the following 10 members:

DXP_synthase_N E1_dh PDH_E1_M POR_N TPP_enzyme_C TPP_enzyme_N Transket_pyr Transketolase_N XFP XFP_N


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...

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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.

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

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

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Representative proteomes UniProt

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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.

Representative proteomes UniProt
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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...


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: transketolaseD2; transket_pyr;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Finn RD , Griffiths-Jones SR
Number in seed: 80
Number in full: 52255
Average length of the domain: 177.1 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 29.08 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 178
Family (HMM) version: 27
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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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The tree shows the occurrence of this domain across different species. More...


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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 Transket_pyr domain has been found. There are 307 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
A0A044T875 View 3D Structure Click here
A0A044U530 View 3D Structure Click here
A0A044VFT7 View 3D Structure Click here
A0A077YWH4 View 3D Structure Click here
A0A077YZY7 View 3D Structure Click here
A0A077ZCG5 View 3D Structure Click here
A0A077ZDF0 View 3D Structure Click here
A0A077ZEL4 View 3D Structure Click here
A0A0D2E2N3 View 3D Structure Click here
A0A0D2ESS2 View 3D Structure Click here
A0A0D2F341 View 3D Structure Click here
A0A0D2F4M0 View 3D Structure Click here
A0A0D2GER0 View 3D Structure Click here
A0A0D2GHN3 View 3D Structure Click here
A0A0D2GIS5 View 3D Structure Click here
A0A0D2GSG8 View 3D Structure Click here
A0A0D2H521 View 3D Structure Click here
A0A0D2HNS2 View 3D Structure Click here
A0A0H3GIT5 View 3D Structure Click here
A0A0H3GJ34 View 3D Structure Click here
A0A0H3GL45 View 3D Structure Click here
A0A0H3GQ15 View 3D Structure Click here
A0A0H3GQ95 View 3D Structure Click here
A0A0H3GW02 View 3D Structure Click here
A0A0H3GY70 View 3D Structure Click here
A0A0H5S5J7 View 3D Structure Click here
A0A0K0E7T0 View 3D Structure Click here
A0A0K0E926 View 3D Structure Click here
A0A0K0EBN5 View 3D Structure Click here
A0A0K0EJZ8 View 3D Structure Click here
A0A0K0ELK5 View 3D Structure Click here
A0A0K0ENA2 View 3D Structure Click here
A0A0K0IYT1 View 3D Structure Click here
A0A0N4U5M6 View 3D Structure Click here
A0A0N4U862 View 3D Structure Click here
A0A0N4UAV3 View 3D Structure Click here
A0A0N4UAV4 View 3D Structure Click here
A0A0P0W9W2 View 3D Structure Click here
A0A0R0FHC7 View 3D Structure Click here
A0A0R0G7H4 View 3D Structure Click here