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129  structures 8464  species 0  interactions 13354  sequences 80  architectures

Family: NAD_kinase_C (PF20143)

Summary: ATP-NAD kinase C-terminal domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

ATP-NAD kinase C-terminal domain Provide feedback

Members of this family include ATP-NAD kinases EC:2.7.1.23, which catalyses the phosphorylation of NAD to NADP utilising ATP and other nucleoside triphosphates as well as inorganic polyphosphate as a source of phosphorus. Also includes NADH kinases EC:2.7.1.86. This entry represents the C-terminal beta sandwich domain.

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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Pfam Clan

This family is a member of clan NAD_kinase_C (CL0701), which has the following description:

This superfamily includes families that are related to the C-terminal beta sandwich domain of NAD kinase. It includes the YegS C-terminal domain, the accessory domains from Diacylglycerol kinase and the ceramide kinase C-terminal domain.

The clan contains the following 4 members:

CERK_C DAGK_acc NAD_kinase_C YegS_C

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
(16)
Full
(13354)
Representative proteomes UniProt
(52354)
RP15
(1891)
RP35
(6291)
RP55
(12695)
RP75
(20916)
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
(16)
Full
(13354)
Representative proteomes UniProt
(52354)
RP15
(1891)
RP35
(6291)
RP55
(12695)
RP75
(20916)
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
(16)
Full
(13354)
Representative proteomes UniProt
(52354)
RP15
(1891)
RP35
(6291)
RP55
(12695)
RP75
(20916)
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

Seed source: Pfam-B_797 (release 4.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Wood V
Number in seed: 16
Number in full: 13354
Average length of the domain: 125.4 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 34.2 %

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 23.7 23.7
Trusted cut-off 23.7 23.8
Noise cut-off 23.6 23.2
Model length: 126
Family (HMM) version: 2
Download: download the raw HMM for this family

Species distribution

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

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 NAD_kinase_C domain has been found. There are 129 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
A0A0D2D9B5 View 3D Structure Click here
A0A0D2EM53 View 3D Structure Click here
A0A0D2H615 View 3D Structure Click here
A0A0H3GU51 View 3D Structure Click here
A0A175W965 View 3D Structure Click here
A0A175WBQ0 View 3D Structure Click here
A0A175WCH6 View 3D Structure Click here
A0A1C1C9M3 View 3D Structure Click here
A0A1C1CIW5 View 3D Structure Click here
A0A1C1D1U6 View 3D Structure Click here
A0A1D6EH53 View 3D Structure Click here
A0A1D6N0S6 View 3D Structure Click here
A0A1D6QLU5 View 3D Structure Click here
A0A1D8PKE0 View 3D Structure Click here
A0A3Q0KJE1 View 3D Structure Click here
A0L8H9 View 3D Structure Click here
A0LG64 View 3D Structure Click here
A1BJI4 View 3D Structure Click here
A1K8P2 View 3D Structure Click here
A1TT64 View 3D Structure Click here
A1VKP7 View 3D Structure Click here
A1W4H1 View 3D Structure Click here
A1WGS0 View 3D Structure Click here
A1WX34 View 3D Structure Click here
A1Z9F4 View 3D Structure Click here
A2SL48 View 3D Structure Click here
A2SQJ8 View 3D Structure Click here
A3DDM2 View 3D Structure Click here
A3QGP1 View 3D Structure Click here
A4J3G3 View 3D Structure Click here
A4SGU4 View 3D Structure Click here
A4XWI3 View 3D Structure Click here
A5D2Z8 View 3D Structure Click here
A5N7J4 View 3D Structure Click here
A5V6G8 View 3D Structure Click here
A5VJ17 View 3D Structure Click here
A6H1D1 View 3D Structure Click here
A6TCM2 View 3D Structure Click here
A7GXF7 View 3D Structure Click here
A7HWM6 View 3D Structure Click here