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609  structures 8293  species 0  interactions 37963  sequences 229  architectures

Family: TPP_enzyme_N (PF02776)

Summary: Thiamine pyrophosphate enzyme, N-terminal TPP 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.

Thiamine pyrophosphate enzyme, N-terminal TPP binding domain Provide feedback

No Pfam abstract.

Literature references

  1. Arjunan P, Umland T, Dyda F, Swaminathan S, Furey W, Sax M, Farrenkopf B, Gao Y, Zhang D, Jordan F; , J Mol Biol 1996;256:590-600.: Crystal structure of the thiamin diphosphate-dependent enzyme pyruvate decarboxylase from the yeast Saccharomyces cerevisiae at 2.3 A resolution. PUBMED:8604141 EPMC:8604141


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR012001

A number of enzymes require thiamine pyrophosphate (TPP) (vitamin B1) as a cofactor. It has been shown [ PUBMED:8604141 ] that some of these enzymes are structurally related. This represents the N-terminal TPP binding domain of TPP enzymes.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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

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
(75)
Full
(37963)
Representative proteomes UniProt
(176345)
RP15
(4192)
RP35
(16529)
RP55
(37336)
RP75
(67240)
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
(75)
Full
(37963)
Representative proteomes UniProt
(176345)
RP15
(4192)
RP35
(16529)
RP55
(37336)
RP75
(67240)
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
(75)
Full
(37963)
Representative proteomes UniProt
(176345)
RP15
(4192)
RP35
(16529)
RP55
(37336)
RP75
(67240)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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: TPP_enzymes_N;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Griffiths-Jones SR
Number in seed: 75
Number in full: 37963
Average length of the domain: 169.50 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 29.57 %

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 26.8 26.8
Trusted cut-off 26.8 26.8
Noise cut-off 26.7 26.7
Model length: 172
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Viroids Viroids Unclassified sequence Unclassified sequence

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 TPP_enzyme_N domain has been found. There are 609 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
A0A0P0V4F6 View 3D Structure Click here
A0A0P0W9X0 View 3D Structure Click here
A0A0R0F259 View 3D Structure Click here
A0A0R0GLC6 View 3D Structure Click here
A0A0R0KAA8 View 3D Structure Click here
A0A0R0KF48 View 3D Structure Click here
A0A0R0KKW5 View 3D Structure Click here
A0A0R4J2I4 View 3D Structure Click here
A0A0R4J3M4 View 3D Structure Click here
A0A1D6FF26 View 3D Structure Click here
A0A1D6FS81 View 3D Structure Click here
A0A1D6HBM9 View 3D Structure Click here
A0A1D6IP62 View 3D Structure Click here
A0A1D6K3R6 View 3D Structure Click here
A0A1D8PJF9 View 3D Structure Click here
A0A1D8PLD6 View 3D Structure Click here
A0A368UI94 View 3D Structure Click here
A0JZP6 View 3D Structure Click here
A0KFN8 View 3D Structure Click here
A0QRG5 View 3D Structure Click here
A0R480 View 3D Structure Click here
A1BI74 View 3D Structure Click here
A1L0T0 View 3D Structure Click here
A1R996 View 3D Structure Click here
A1SBA6 View 3D Structure Click here
A1SE17 View 3D Structure Click here
A1SRV2 View 3D Structure Click here
A1T3R3 View 3D Structure Click here
A1UAX3 View 3D Structure Click here
A1WW41 View 3D Structure Click here
A2XFI3 View 3D Structure Click here
A2Y5L9 View 3D Structure Click here
A2YQ76 View 3D Structure Click here
A3BFW9 View 3D Structure Click here
A3N348 View 3D Structure Click here
A3PBY1 View 3D Structure Click here
A3QJ17 View 3D Structure Click here
A3SR25 View 3D Structure Click here
A4FPV1 View 3D Structure Click here
A4I3N7 View 3D Structure Click here