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13  structures 1375  species 0  interactions 4061  sequences 46  architectures

Family: CBFB_NFYA (PF02045)

Summary: CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B

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CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001289

Diverse DNA binding proteins are known to bind the CCAAT box, a common cis- acting element found in the promoter and enhancer regions of a large number of genes in eukaryotes. Amongst these proteins is one known as the CCAAT-binding factor (CBF) or nuclear transcription factor Y (NF-Y) [ PUBMED:1549471 ]. CBF is a heteromeric transcription factor that consists of two different components both needed for DNA-binding.

The HAP protein complex of yeast binds to the upstream activation site of cytochrome C iso-1 gene (CYC1) as well as other genes involved in mitochondrial electron transport and activates their expression. It also recognises the sequence CCAAT and is structurally and evolutionary related to CBF.

The first subunit of CBF is known as CBF-A or NF-YB in vertebrates, and HAP3 in budding yeast. The second subunit is known as CBF-B or NF-YA in vertebrates and HAP2 in budding yeast. It is a protein of 265 to 350 amino-acid residues which contains a highly conserved region of about 60 residues. This region, called the 'essential core' [ PUBMED:1899284 ], seems to consist of two subdomains: an N-terminal subunit-association domain and a C-terminal DNA recognition domain.

This entry represents the NF-YA subunit.

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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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...

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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.

  Seed
(56)
Full
(4061)
Representative proteomes UniProt
(6225)
RP15
(615)
RP35
(1822)
RP55
(3250)
RP75
(4325)
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PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(56)
Full
(4061)
Representative proteomes UniProt
(6225)
RP15
(615)
RP35
(1822)
RP55
(3250)
RP75
(4325)
Alignment:
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Sequence:
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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
(56)
Full
(4061)
Representative proteomes UniProt
(6225)
RP15
(615)
RP35
(1822)
RP55
(3250)
RP75
(4325)
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: IPR001289
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Mian N , Bateman A
Number in seed: 56
Number in full: 4061
Average length of the domain: 55.50 aa
Average identity of full alignment: 67 %
Average coverage of the sequence by the domain: 18.72 %

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 27.9 27.1
Noise cut-off 26.6 26.5
Model length: 56
Family (HMM) version: 18
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

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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 CBFB_NFYA domain has been found. There are 13 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
A0A0N7KG67 View 3D Structure Click here
A0A0N7KMY8 View 3D Structure Click here
A0A0P0W2B5 View 3D Structure Click here
A0A0R0FVT3 View 3D Structure Click here
A0A0R0H9K2 View 3D Structure Click here
A0A1D6F9G6 View 3D Structure Click here
A0A1D6GK51 View 3D Structure Click here
A0A1D6HLV3 View 3D Structure Click here
A0A1D6JEF6 View 3D Structure Click here
A0A1D6JQA0 View 3D Structure Click here
A0A1D6K5I2 View 3D Structure Click here
A0A1D6K5T2 View 3D Structure Click here
A0A1D6MWG6 View 3D Structure Click here
A0A1D8PE35 View 3D Structure Click here
A5PMG5 View 3D Structure Click here
B4F9M3 View 3D Structure Click here
B4FHR0 View 3D Structure Click here
B4FIN9 View 3D Structure Click here
B4FNM1 View 3D Structure Click here
B6TAR1 View 3D Structure Click here
C0PNR4 View 3D Structure Click here
C6TD07 View 3D Structure Click here
C6TG32 View 3D Structure Click here
E0WC41 View 3D Structure Click here
E9QGB7 View 3D Structure Click here
G5EEG1 View 3D Structure Click here
I1JQA1 View 3D Structure Click here
I1K472 View 3D Structure Click here
I1KSM7 View 3D Structure Click here
I1KYS9 View 3D Structure Click here
I1L1N5 View 3D Structure Click here
I1LY31 View 3D Structure Click here
I1M0X4 View 3D Structure Click here
I1M6C1 View 3D Structure Click here
I1MG33 View 3D Structure Click here
I1MHB5 View 3D Structure Click here
K7K9J7 View 3D Structure Click here
K7LBF6 View 3D Structure Click here
K7LI34 View 3D Structure Click here
K7MEE6 View 3D Structure Click here