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62  structures 1708  species 0  interactions 12867  sequences 187  architectures

Family: CBFD_NFYB_HMF (PF00808)

Summary: Histone-like transcription factor (CBF/NF-Y) and archaeal histone

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.

Histone-like transcription factor (CBF/NF-Y) and archaeal histone Provide feedback

This family includes archaebacterial histones and histone like transcription factors from eukaryotes.

Literature references

  1. Burley SK, Xie X, Clark KL, Shu F; , Curr Opin Struct Biol 1997;7:94-102.: Histone-like transcription factors in eukaryotes. PUBMED:9032065 EPMC:9032065


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003958

This domain is found in archaebacterial histones and histone-like transcription factors from eukaryotes.

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 Histone (CL0012), which has the following description:

Members of this clan all possess a histone fold. Generally proteins in this clan are DNA binding.

The clan contains the following 17 members:

Bromo_TP Bromo_TP_like CBFD_NFYB_HMF CENP-S CENP-T_C CENP-W CENP-X DUF1931 Histone PAF TAF TAF4 TAFII28 TFIID-18kDa TFIID-31kDa TFIID_20kDa TFIID_30kDa

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
(25)
Full
(12867)
Representative proteomes UniProt
(23084)
RP15
(2294)
RP35
(6425)
RP55
(10496)
RP75
(14149)
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
(25)
Full
(12867)
Representative proteomes UniProt
(23084)
RP15
(2294)
RP35
(6425)
RP55
(10496)
RP75
(14149)
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
(25)
Full
(12867)
Representative proteomes UniProt
(23084)
RP15
(2294)
RP35
(6425)
RP55
(10496)
RP75
(14149)
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_1351 (Rel 2.1) & Pfam-B_3673 (Rel 7.5) & Pfam-B_2078 (Rel 8.0)
Previous IDs: Archael_histone; Arch_histone;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 25
Number in full: 12867
Average length of the domain: 64.20 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 30.35 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.4 21.4
Trusted cut-off 21.4 21.4
Noise cut-off 21.3 21.3
Model length: 65
Family (HMM) version: 25
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 CBFD_NFYB_HMF domain has been found. There are 62 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
A0A060D557 View 3D Structure Click here
A0A096R9U6 View 3D Structure Click here
A0A0G2L1F4 View 3D Structure Click here
A0A0K2CT95 View 3D Structure Click here
A0A0N7KPF9 View 3D Structure Click here
A0A0P0VCF9 View 3D Structure Click here
A0A0P0XQL1 View 3D Structure Click here
A0A0R0EXD2 View 3D Structure Click here
A0A0R0F8V1 View 3D Structure Click here
A0A0R0G186 View 3D Structure Click here
A0A0R0H2E8 View 3D Structure Click here
A0A0R0HSF8 View 3D Structure Click here
A0A0R0I959 View 3D Structure Click here
A0A0R0IEV2 View 3D Structure Click here
A0A0R0JBL0 View 3D Structure Click here
A0A0R0JYX8 View 3D Structure Click here
A0A0R0KAB8 View 3D Structure Click here
A0A0R0KIC7 View 3D Structure Click here
A0A0R0KT72 View 3D Structure Click here
A0A0R0KTG7 View 3D Structure Click here
A0A0R0KUF3 View 3D Structure Click here
A0A0R0KWV4 View 3D Structure Click here
A0A0R4J2T6 View 3D Structure Click here
A0A0R4J671 View 3D Structure Click here
A0A1D6DSP3 View 3D Structure Click here
A0A1D6F122 View 3D Structure Click here
A0A1D6FKV4 View 3D Structure Click here
A0A1D6FS52 View 3D Structure Click here
A0A1D6G4V6 View 3D Structure Click here
A0A1D6G8R8 View 3D Structure Click here
A0A1D6HJ17 View 3D Structure Click here
A0A1D6HV39 View 3D Structure Click here
A0A1D6IJ69 View 3D Structure Click here
A0A1D6K5M3 View 3D Structure Click here
A0A1D6LQ42 View 3D Structure Click here
A0A1D6M656 View 3D Structure Click here
A0A1D6M765 View 3D Structure Click here
A0A1D6MLX8 View 3D Structure Click here
A0A1D6N242 View 3D Structure Click here
A0A1D6N7R4 View 3D Structure Click here
A0A1D8PG40 View 3D Structure Click here
A0A1D8PLA9 View 3D Structure Click here
A0A1D8PLM5 View 3D Structure Click here
A0A2R8PWV4 View 3D Structure Click here
A0A368UIJ8 View 3D Structure Click here
A0JPP1 View 3D Structure Click here
A4HSP4 View 3D Structure Click here
A4HW98 View 3D Structure Click here
A4IA16 View 3D Structure Click here
A9Z055 View 3D Structure Click here
B4F864 View 3D Structure Click here
B4FFQ8 View 3D Structure Click here
B4FLF9 View 3D Structure Click here
B4FWZ1 View 3D Structure Click here
B5KMS8 View 3D Structure Click here
B5KMS9 View 3D Structure Click here
B6SII8 View 3D Structure Click here
B6TCI2 View 3D Structure Click here
B6TI74 View 3D Structure Click here
B6UA50 View 3D Structure Click here
C6SZ53 View 3D Structure Click here
C6TNG0 View 3D Structure Click here
C6Y4D0 View 3D Structure Click here
D3Z9P5 View 3D Structure Click here
D3ZAR9 View 3D Structure Click here
E0WC42 View 3D Structure Click here
F1R8S0 View 3D Structure Click here
F1RCI6 View 3D Structure Click here
F4K162 View 3D Structure Click here
F6NIX9 View 3D Structure Click here
G2TRL2 View 3D Structure Click here
H9B3R6 View 3D Structure Click here
I1K186 View 3D Structure Click here
I1K511 View 3D Structure Click here
I1KC24 View 3D Structure Click here
I1KFK3 View 3D Structure Click here
I1KTG9 View 3D Structure Click here
I1KTY0 View 3D Structure Click here
I1KYJ4 View 3D Structure Click here
I1L037 View 3D Structure Click here
I1L7X0 View 3D Structure Click here
I1LL70 View 3D Structure Click here
I1LRH0 View 3D Structure Click here
I1LUT9 View 3D Structure Click here
I1M0K0 View 3D Structure Click here
I1M133 View 3D Structure Click here
I1M135 View 3D Structure Click here
I1M3F6 View 3D Structure Click here
I1MIK6 View 3D Structure Click here
I1MRH0 View 3D Structure Click here
I1MUI1 View 3D Structure Click here
I1MYF9 View 3D Structure Click here
I1NCV5 View 3D Structure Click here
I1NIX7 View 3D Structure Click here
K7KDQ4 View 3D Structure Click here
K7KDZ5 View 3D Structure Click here
K7KGQ0 View 3D Structure Click here
K7KR11 View 3D Structure Click here
K7L2H0 View 3D Structure Click here
K7L3Q0 View 3D Structure Click here
K7L6M6 View 3D Structure Click here
K7LBT7 View 3D Structure Click here
K7LHH3 View 3D Structure Click here
K7LJK2 View 3D Structure Click here
K7LYA1 View 3D Structure Click here
K7M0W9 View 3D Structure Click here
K7M4T4 View 3D Structure Click here
K7MS80 View 3D Structure Click here
K7MZZ0 View 3D Structure Click here
K7N593 View 3D Structure Click here
K7TT56 View 3D Structure Click here
K7U824 View 3D Structure Click here
K7UZ84 View 3D Structure Click here
K7V395 View 3D Structure Click here
K7V8D5 View 3D Structure Click here
O04027 View 3D Structure Click here
O14348 View 3D Structure Click here
O17072 View 3D Structure Click here
O17286 View 3D Structure Click here
O23310 View 3D Structure Click here
O45550 View 3D Structure Click here
O82248 View 3D Structure Click here
P13434 View 3D Structure Click here
P25208 View 3D Structure Click here
P25209 View 3D Structure Click here
P36611 View 3D Structure Click here
P40096 View 3D Structure Click here
P49592 View 3D Structure Click here
P63139 View 3D Structure Click here
P63140 View 3D Structure Click here
P79007 View 3D Structure Click here
P87174 View 3D Structure Click here
Q01658 View 3D Structure Click here
Q08BR1 View 3D Structure Click here
Q0DJB5 View 3D Structure Click here
Q0J0W2 View 3D Structure Click here
Q0J7P4 View 3D Structure Click here
Q10315 View 3D Structure Click here
Q10AH3 View 3D Structure Click here
Q14919 View 3D Structure Click here
Q20237 View 3D Structure Click here
Q22798 View 3D Structure Click here
Q2R2Z2 View 3D Structure Click here
Q4D3L1 View 3D Structure Click here
Q4DTC9 View 3D Structure Click here
Q4E592 View 3D Structure Click here
Q4PSE2 View 3D Structure Click here
Q54DA1 View 3D Structure Click here
Q54WV0 View 3D Structure Click here
Q557I1 View 3D Structure Click here
Q55DJ5 View 3D Structure Click here
Q55GE1 View 3D Structure Click here
Q561X4 View 3D Structure Click here
Q57632 View 3D Structure Click here
Q58342 View 3D Structure Click here
Q58655 View 3D Structure Click here
Q58CM8 View 3D Structure Click here
Q59041 View 3D Structure Click here
Q5A0I6 View 3D Structure Click here
Q5A6N7 View 3D Structure Click here
Q5AHY9 View 3D Structure Click here
Q5QMG3 View 3D Structure Click here
Q5VNF4 View 3D Structure Click here
Q5VRY6 View 3D Structure Click here
Q5XI68 View 3D Structure Click here
Q60264 View 3D Structure Click here
Q60EQ4 View 3D Structure Click here
Q642A5 View 3D Structure Click here
Q65X80 View 3D Structure Click here
Q65XK1 View 3D Structure Click here
Q67XJ2 View 3D Structure Click here
Q69J40 View 3D Structure Click here
Q6PBL4 View 3D Structure Click here
Q6Z348 View 3D Structure Click here
Q6ZFM9 View 3D Structure Click here
Q75IZ7 View 3D Structure Click here
Q75JQ9 View 3D Structure Click here
Q7KWN0 View 3D Structure Click here
Q84W66 View 3D Structure Click here
Q8IDB5 View 3D Structure Click here
Q8IEN4 View 3D Structure Click here
Q8IHQ2 View 3D Structure Click here
Q8L4B2 View 3D Structure Click here
Q8ST61 View 3D Structure Click here
Q8VYK4 View 3D Structure Click here
Q8W0W5 View 3D Structure Click here
Q8W0W6 View 3D Structure Click here
Q91WV0 View 3D Structure Click here
Q92317 View 3D Structure Click here
Q942Y5 View 3D Structure Click here
Q944I5 View 3D Structure Click here
Q94EJ7 View 3D Structure Click here
Q9CQ36 View 3D Structure Click here
Q9D6N5 View 3D Structure Click here
Q9FGJ3 View 3D Structure Click here
Q9FGP6 View 3D Structure Click here
Q9FGP7 View 3D Structure Click here
Q9FGP8 View 3D Structure Click here
Q9FHS0 View 3D Structure Click here
Q9FMV5 View 3D Structure Click here
Q9JKP7 View 3D Structure Click here
Q9JKP8 View 3D Structure Click here
Q9LHG0 View 3D Structure Click here
Q9LN09 View 3D Structure Click here
Q9NAC5 View 3D Structure Click here
Q9NR33 View 3D Structure Click here
Q9NRF9 View 3D Structure Click here
Q9NRG0 View 3D Structure Click here
Q9SFD8 View 3D Structure Click here
Q9SIT9 View 3D Structure Click here
Q9SLG0 View 3D Structure Click here
Q9SMP0 View 3D Structure Click here
Q9V444 View 3D Structure Click here
Q9V452 View 3D Structure Click here
Q9VJQ5 View 3D Structure Click here
Q9W256 View 3D Structure Click here
Q9W2E3 View 3D Structure Click here
Q9W3V9 View 3D Structure Click here
Q9XE33 View 3D Structure Click here
Q9ZQH2 View 3D Structure Click here
Q9ZVL3 View 3D Structure Click here