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14  structures 7035  species 0  interactions 8332  sequences 23  architectures

Family: GPD_NAD_C_bact (PF20618)

Summary: Bacterial GPD, NAD-dependent C-terminal

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Bacterial GPD, NAD-dependent C-terminal Provide feedback

This is the C-terminal domain of NAD-dependent glycerol-3-phosphate dehydrogenase (GPD) from bacteria and archaea. GPD catalyses the reversible reduction of dihydroxyacetone phosphate to glycerol-3-phosphate.

Internal 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 (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
(99)
Full
(8332)
Representative proteomes UniProt
(39238)
RP15
(1166)
RP35
(4133)
RP55
(8669)
RP75
(14778)
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
(99)
Full
(8332)
Representative proteomes UniProt
(39238)
RP15
(1166)
RP35
(4133)
RP55
(8669)
RP75
(14778)
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
(99)
Full
(8332)
Representative proteomes UniProt
(39238)
RP15
(1166)
RP35
(4133)
RP55
(8669)
RP75
(14778)
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

This family is new in this Pfam release.

Seed source: MGnify-UniProt clustering
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Paysan-Lafosse T , Chuguransky S
Number in seed: 99
Number in full: 8332
Average length of the domain: 66.6 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 19.66 %

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 27.6 27.6
Trusted cut-off 27.6 27.6
Noise cut-off 27.5 27.5
Model length: 66
Family (HMM) version: 1
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

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 GPD_NAD_C_bact domain has been found. There are 14 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
A0A0H3GUQ5 View 3D Structure Click here
A0A0K0ECC0 View 3D Structure Click here
A0A1D6HW80 View 3D Structure Click here
A0KF08 View 3D Structure Click here
A0LLR7 View 3D Structure Click here
A1AXJ0 View 3D Structure Click here
A1B3J7 View 3D Structure Click here
A1BJJ1 View 3D Structure Click here
A1S1L9 View 3D Structure Click here
A1SZH9 View 3D Structure Click here
A1TTW1 View 3D Structure Click here
A1UTZ3 View 3D Structure Click here
A1VKS0 View 3D Structure Click here
A1WBI9 View 3D Structure Click here
A1WDX8 View 3D Structure Click here
A1WWC7 View 3D Structure Click here
A2SDP0 View 3D Structure Click here
A3CQT0 View 3D Structure Click here
A3N2F8 View 3D Structure Click here
A3QJM1 View 3D Structure Click here
A4G993 View 3D Structure Click here
A4HUG3 View 3D Structure Click here
A4J3P3 View 3D Structure Click here
A4VY17 View 3D Structure Click here
A4XV57 View 3D Structure Click here
A4YK34 View 3D Structure Click here
A5CE97 View 3D Structure Click here
A5D1U4 View 3D Structure Click here
A5FYL0 View 3D Structure Click here
A5GTA8 View 3D Structure Click here
A5VIG6 View 3D Structure Click here
A6Q3B2 View 3D Structure Click here
A6TFK3 View 3D Structure Click here
A7HST0 View 3D Structure Click here
A8ARJ5 View 3D Structure Click here
A8AUM5 View 3D Structure Click here
A8FEL7 View 3D Structure Click here
A8HAD7 View 3D Structure Click here
A8IJ80 View 3D Structure Click here
A8L577 View 3D Structure Click here