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0  structures 55  species 0  interactions 920  sequences 9  architectures

Family: ZF-HD_dimer (PF04770)

Summary: ZF-HD protein dimerisation region

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ZF-HD protein dimerisation region Provide feedback

This family of proteins has are plant transcription factors, and have been named ZF-HD for zinc finger homeodomain proteins, on the basis of similarity to proteins of known structure [1]. This region is thought to be involved in the formation of homo and heterodimers, and may form a zinc finger [1].

Literature references

  1. Windhovel A, Hein I, Dabrowa R, Stockhaus J; , Plant Mol Biol 2001;45:201-214.: Characterization of a novel class of plant homeodomain proteins that bind to the C4 phosphoenolpyruvate carboxylase gene of Flaveria trinervia. PUBMED:11289511 EPMC:11289511


This tab holds annotation information from the InterPro database.

InterPro entry IPR006456

The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors. HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development [PUBMED:16428600]. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [PUBMED:11289511] and in pathogen signaling and plant defense mechanisms [PUBMED:17485478].

These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers [PUBMED:11289511].

This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in INTERPRO.

Domain organisation

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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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(65)
Full
(920)
Representative proteomes UniProt
(1191)
NCBI
(1838)
Meta
(0)
RP15
(72)
RP35
(451)
RP55
(791)
RP75
(944)
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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
(65)
Full
(920)
Representative proteomes UniProt
(1191)
NCBI
(1838)
Meta
(0)
RP15
(72)
RP35
(451)
RP55
(791)
RP75
(944)
Alignment:
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Sequence:
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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
(65)
Full
(920)
Representative proteomes UniProt
(1191)
NCBI
(1838)
Meta
(0)
RP15
(72)
RP35
(451)
RP55
(791)
RP75
(944)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   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_2002 (release 7.6)
Previous IDs: none
Type: Family
Author: Kerrison ND
Number in seed: 65
Number in full: 920
Average length of the domain: 54.00 aa
Average identity of full alignment: 59 %
Average coverage of the sequence by the domain: 23.38 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.4 19.4
Trusted cut-off 19.5 21.9
Noise cut-off 18.6 19.0
Model length: 55
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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