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2  structures 184  species 0  interactions 5514  sequences 55  architectures

Family: NAF (PF03822)

Summary: NAF domain

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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.

NAF domain Provide feedback

No Pfam abstract.

Literature references

  1. Albrecht V, Ritz O, Linder S, Harter K, Kudla J; , EMBO J 2001;20:1051-1063.: The NAF domain defines a novel protein-protein interaction module conserved in Ca2+-regulated kinases. PUBMED:11230129 EPMC:11230129


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004041

The NAF domain is a 24 amino acid domain that is found in a plant-specific subgroup of serine-threonine protein kinases (CIPKs), that interact with calcineurin B-like calcium sensor proteins (CBLs). Whereas the N-terminal part of CIPKs comprises a conserved catalytic domain typical of Ser-Thr kinases, the much less conserved C-terminal domain appears to be unique to this subgroup of kinases. The only exception is the NAF domain that forms an 'island of conservation' in this otherwise variable region. The NAF domain has been named after the prominent conserved amino acids Asn-Ala-Phe. It represents a minimum protein interaction module that is both necessary and sufficient to mediate the interaction with the CBL calcium sensor proteins [ PUBMED:11230129 ].

The secondary structure of the NAF domain is currently not known, but secondary structure computation of the C-terminal region of Arabidopsis thaliana CBL-interacting protein kinase 1 revealed a long helical structure [ PUBMED:11230129 ].

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 KA1-like (CL0573), which has the following description:

This superfamily is characterised by small adenylate-sensing domains at the C-terminus of molecules such as AMP-Activated Protein Kinases an SNF1-like protein kinases [1].

The clan contains the following 4 members:

AdenylateSensor KA1 NAF NAM-associated

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
(142)
Full
(5514)
Representative proteomes UniProt
(8420)
RP15
(658)
RP35
(2663)
RP55
(4718)
RP75
(6192)
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
(142)
Full
(5514)
Representative proteomes UniProt
(8420)
RP15
(658)
RP35
(2663)
RP55
(4718)
RP75
(6192)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(142)
Full
(5514)
Representative proteomes UniProt
(8420)
RP15
(658)
RP35
(2663)
RP55
(4718)
RP75
(6192)
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: PROSITE
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Griffiths-Jones SR
Number in seed: 142
Number in full: 5514
Average length of the domain: 59.00 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 13.66 %

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 25.0 25.0
Trusted cut-off 25.0 25.3
Noise cut-off 24.9 24.9
Model length: 54
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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 NAF domain has been found. There are 2 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
A0A0B4J3D8 View 3D Structure Click here
A0A0N7KHM3 View 3D Structure Click here
A0A0N7KIK3 View 3D Structure Click here
A0A0P0W736 View 3D Structure Click here
A0A0P0XYW4 View 3D Structure Click here
A0A0R0EX69 View 3D Structure Click here
A0A0R0F327 View 3D Structure Click here
A0A0R0F950 View 3D Structure Click here
A0A0R0FME7 View 3D Structure Click here
A0A0R0G3C2 View 3D Structure Click here
A0A0R0GQL4 View 3D Structure Click here
A0A0R0GT71 View 3D Structure Click here
A0A0R0HUY3 View 3D Structure Click here
A0A0R0IBP3 View 3D Structure Click here
A0A0R0IC52 View 3D Structure Click here
A0A0R0IS44 View 3D Structure Click here
A0A0R0JCR2 View 3D Structure Click here
A0A0R0L077 View 3D Structure Click here
A0A0R4J2Q3 View 3D Structure Click here
A0A0R4J2Q6 View 3D Structure Click here
A0A0R4J3S3 View 3D Structure Click here
A0A0R4J3Z4 View 3D Structure Click here
A0A0R4J5V6 View 3D Structure Click here
A0A1D6DQ40 View 3D Structure Click here
A0A1D6EPU8 View 3D Structure Click here
A0A1D6F284 View 3D Structure Click here
A0A1D6F3T5 View 3D Structure Click here
A0A1D6F4E3 View 3D Structure Click here
A0A1D6FG83 View 3D Structure Click here
A0A1D6HSH6 View 3D Structure Click here
A0A1D6IKR8 View 3D Structure Click here
A0A1D6IP00 View 3D Structure Click here
A0A1D6ISZ4 View 3D Structure Click here
A0A1D6ISZ7 View 3D Structure Click here
A0A1D6IT01 View 3D Structure Click here
A0A1D6LS89 View 3D Structure Click here
A0A1D6MW08 View 3D Structure Click here
A0A1D6N844 View 3D Structure Click here
A0A1D6NB16 View 3D Structure Click here
A0A1D6NN49 View 3D Structure Click here