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0  structures 158  species 0  interactions 5765  sequences 42  architectures

Family: zf-Dof (PF02701)

Summary: Dof domain, zinc finger

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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.

Dof domain, zinc finger Provide feedback

The Dof domain is a zinc finger DNA-binding domain, that shows resemblance to the Cys2 zinc finger [1].

Literature references

  1. Shimofurutani N, Kisu Y, Suzuki M, Esaka M; , FEBS Lett 1998;430:251-256.: Functional analyses of the Dof domain, a zinc finger DNA-binding domain, in a pumpkin DNA-binding protein AOBP. PUBMED:9688549 EPMC:9688549


This tab holds annotation information from the InterPro database.

InterPro entry IPR003851

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [ PUBMED:10529348 , PUBMED:15963892 , PUBMED:15718139 , PUBMED:17210253 , PUBMED:12665246 ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few [ PUBMED:11179890 ]. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.

This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved [ PUBMED:9688549 ]. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants.

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...

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
(44)
Full
(5765)
Representative proteomes UniProt
(8838)
RP15
(562)
RP35
(3119)
RP55
(4780)
RP75
(6397)
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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
(44)
Full
(5765)
Representative proteomes UniProt
(8838)
RP15
(562)
RP35
(3119)
RP55
(4780)
RP75
(6397)
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
(44)
Full
(5765)
Representative proteomes UniProt
(8838)
RP15
(562)
RP35
(3119)
RP55
(4780)
RP75
(6397)
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_1250 (release 5.5)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Mian N , Bateman A
Number in seed: 44
Number in full: 5765
Average length of the domain: 58.20 aa
Average identity of full alignment: 70 %
Average coverage of the sequence by the domain: 18.54 %

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 26.6 26.6
Trusted cut-off 26.6 26.7
Noise cut-off 26.5 26.4
Model length: 59
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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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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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
A0A060CY74 View 3D Structure Click here
A0A060D121 View 3D Structure Click here
A0A060D249 View 3D Structure Click here
A0A060D4H1 View 3D Structure Click here
A0A060D5A5 View 3D Structure Click here
A0A060D5B9 View 3D Structure Click here
A0A0N7KDH5 View 3D Structure Click here
A0A0P0V0N4 View 3D Structure Click here
A0A0P0V139 View 3D Structure Click here
A0A0P0VAX4 View 3D Structure Click here
A0A0P0W0V5 View 3D Structure Click here
A0A0P0X462 View 3D Structure Click here
A0A0P0XPP6 View 3D Structure Click here
A0A0R0EQ32 View 3D Structure Click here
A0A0R0FLR7 View 3D Structure Click here
A0A0R0G446 View 3D Structure Click here
A0A0R0GQ42 View 3D Structure Click here
A0A0R0HGZ1 View 3D Structure Click here
A0A0R0HUU0 View 3D Structure Click here
A0A0R0J0D5 View 3D Structure Click here
A0A0R0KD59 View 3D Structure Click here
A0A0R0KYP3 View 3D Structure Click here
A0A1D6DT60 View 3D Structure Click here
A0A1D6E2N6 View 3D Structure Click here
A0A1D6ERS9 View 3D Structure Click here
A0A1D6FTB4 View 3D Structure Click here
A0A1D6FVN7 View 3D Structure Click here
A0A1D6GE51 View 3D Structure Click here
A0A1D6GGF9 View 3D Structure Click here
A0A1D6GLQ1 View 3D Structure Click here
A0A1D6GM25 View 3D Structure Click here
A0A1D6GQZ6 View 3D Structure Click here
A0A1D6HFT9 View 3D Structure Click here
A0A1D6I6L4 View 3D Structure Click here
A0A1D6ICL0 View 3D Structure Click here
A0A1D6JC53 View 3D Structure Click here
A0A1D6JY60 View 3D Structure Click here
A0A1D6KE35 View 3D Structure Click here
A0A1D6KVQ3 View 3D Structure Click here
A0A1D6L5W4 View 3D Structure Click here
A0A1D6L9X9 View 3D Structure Click here
A0A1D6LHP6 View 3D Structure Click here
A0A1D6MQD3 View 3D Structure Click here
A0A1D6MQV2 View 3D Structure Click here
A0A1D6MWU4 View 3D Structure Click here
A0A1D6N6H6 View 3D Structure Click here
A0A1D6NG26 View 3D Structure Click here
B0EW02 View 3D Structure Click here
B4FAN2 View 3D Structure Click here
B4FDH4 View 3D Structure Click here
B4FDW7 View 3D Structure Click here
B4FDY8 View 3D Structure Click here
B4FRV3 View 3D Structure Click here
B4FWT7 View 3D Structure Click here
B4FX17 View 3D Structure Click here
B6SQJ6 View 3D Structure Click here
B6SV34 View 3D Structure Click here
B6TLJ4 View 3D Structure Click here
B9F1L8 View 3D Structure Click here
C0HF78 View 3D Structure Click here
C4J8W5 View 3D Structure Click here
C6T5G7 View 3D Structure Click here
C6TGC3 View 3D Structure Click here
C7DQE7 View 3D Structure Click here
F1DJS2 View 3D Structure Click here
I1J936 View 3D Structure Click here
I1JWL7 View 3D Structure Click here
I1JX78 View 3D Structure Click here
I1JZN7 View 3D Structure Click here
I1K158 View 3D Structure Click here
I1KCF8 View 3D Structure Click here
I1KCU1 View 3D Structure Click here
I1KLH3 View 3D Structure Click here
I1KMH1 View 3D Structure Click here
I1KSE1 View 3D Structure Click here
I1KUW8 View 3D Structure Click here
I1KX56 View 3D Structure Click here
I1KZD7 View 3D Structure Click here
I1L4T3 View 3D Structure Click here
I1L5W6 View 3D Structure Click here
I1LHH9 View 3D Structure Click here
I1LR01 View 3D Structure Click here
I1LWK9 View 3D Structure Click here
I1M087 View 3D Structure Click here
I1M0D9 View 3D Structure Click here
I1M220 View 3D Structure Click here
I1M221 View 3D Structure Click here
I1M283 View 3D Structure Click here
I1M4N9 View 3D Structure Click here
I1M5E0 View 3D Structure Click here
I1MDG2 View 3D Structure Click here
I1MEF1 View 3D Structure Click here
I1MEK7 View 3D Structure Click here
I1MEK8 View 3D Structure Click here
I1MER9 View 3D Structure Click here
I1MNL4 View 3D Structure Click here
I1MT95 View 3D Structure Click here
I1MW20 View 3D Structure Click here
I1N2E0 View 3D Structure Click here
I1N4E5 View 3D Structure Click here
I1N654 View 3D Structure Click here
I1NAU1 View 3D Structure Click here
I1NIG5 View 3D Structure Click here
K7K1C7 View 3D Structure Click here
K7K1V7 View 3D Structure Click here
K7K6R9 View 3D Structure Click here
K7K7B3 View 3D Structure Click here
K7K7M1 View 3D Structure Click here
K7KH42 View 3D Structure Click here
K7KKN2 View 3D Structure Click here
K7KLZ8 View 3D Structure Click here
K7KMQ7 View 3D Structure Click here
K7KUP9 View 3D Structure Click here
K7KUU3 View 3D Structure Click here
K7KW99 View 3D Structure Click here
K7KYZ6 View 3D Structure Click here
K7L2R3 View 3D Structure Click here
K7L2R4 View 3D Structure Click here
K7L890 View 3D Structure Click here
K7LI29 View 3D Structure Click here
K7LTC4 View 3D Structure Click here
K7M3D9 View 3D Structure Click here
K7M9L0 View 3D Structure Click here
K7MCW1 View 3D Structure Click here
K7MET1 View 3D Structure Click here
K7MKQ3 View 3D Structure Click here
K7MSC7 View 3D Structure Click here
K7MVD4 View 3D Structure Click here
K7MXY4 View 3D Structure Click here
K7N176 View 3D Structure Click here
K7U893 View 3D Structure Click here
K7UGC9 View 3D Structure Click here
K7UHV4 View 3D Structure Click here
K7V4V2 View 3D Structure Click here
O22967 View 3D Structure Click here
O24463 View 3D Structure Click here
O49550 View 3D Structure Click here
O80928 View 3D Structure Click here
O82155 View 3D Structure Click here
P38564 View 3D Structure Click here
P68349 View 3D Structure Click here
P68350 View 3D Structure Click here
Q0DHU3 View 3D Structure Click here
Q0DM99 View 3D Structure Click here
Q0DY98 View 3D Structure Click here
Q0GLD1 View 3D Structure Click here
Q0IXW1 View 3D Structure Click here
Q10EQ1 View 3D Structure Click here
Q2QND3 View 3D Structure Click here
Q39088 View 3D Structure Click here
Q43385 View 3D Structure Click here
Q5JLR7 View 3D Structure Click here
Q5VNE4 View 3D Structure Click here
Q65XV0 View 3D Structure Click here
Q6K537 View 3D Structure Click here
Q6Z345 View 3D Structure Click here
Q6ZBQ1 View 3D Structure Click here
Q7FAN8 View 3D Structure Click here
Q7G2G1 View 3D Structure Click here
Q84JQ8 View 3D Structure Click here
Q84K52 View 3D Structure Click here
Q84PD2 View 3D Structure Click here
Q84TE9 View 3D Structure Click here
Q8L9V6 View 3D Structure Click here
Q8LAP8 View 3D Structure Click here
Q8LDR0 View 3D Structure Click here
Q8LE43 View 3D Structure Click here
Q8LFV3 View 3D Structure Click here
Q8S7W1 View 3D Structure Click here
Q8W1E3 View 3D Structure Click here
Q93ZL5 View 3D Structure Click here
Q94AR6 View 3D Structure Click here
Q9FGD6 View 3D Structure Click here
Q9FM03 View 3D Structure Click here
Q9FZA4 View 3D Structure Click here
Q9LQX4 View 3D Structure Click here
Q9LSL6 View 3D Structure Click here
Q9LZ56 View 3D Structure Click here
Q9M161 View 3D Structure Click here
Q9M1E6 View 3D Structure Click here
Q9M2U1 View 3D Structure Click here
Q9SEZ3 View 3D Structure Click here
Q9SUA9 View 3D Structure Click here
Q9SUB0 View 3D Structure Click here
Q9SUB1 View 3D Structure Click here
Q9SVC5 View 3D Structure Click here
Q9SX97 View 3D Structure Click here
Q9SXG8 View 3D Structure Click here
Q9ZPY0 View 3D Structure Click here
Q9ZV33 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;