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0  structures 137  species 0  interactions 1342  sequences 13  architectures

Family: Plant_zn_clust (PF10533)

Summary: Plant zinc cluster domain

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.

Plant zinc cluster domain Provide feedback

This zinc binding domain was identified by Babu and colleagues and found associated with the WRKY domain PF03106 [1].

Literature references

  1. Babu MM, Iyer LM, Balaji S, Aravind L; , Nucleic Acids Res. 2006; [Epub ahead of print]: The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons. PUBMED:17130173 EPMC:17130173


This tab holds annotation information from the InterPro database.

InterPro entry IPR018872

This zinc binding domain is found associated with the WRKY domain INTERPRO [ PUBMED:17130173 ].

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
(34)
Full
(1342)
Representative proteomes UniProt
(2161)
RP15
(112)
RP35
(675)
RP55
(1099)
RP75
(1472)
Jalview View  View  View  View  View  View  View 
HTML View  View           
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
(34)
Full
(1342)
Representative proteomes UniProt
(2161)
RP15
(112)
RP35
(675)
RP55
(1099)
RP75
(1472)
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
(34)
Full
(1342)
Representative proteomes UniProt
(2161)
RP15
(112)
RP35
(675)
RP55
(1099)
RP75
(1472)
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: Iyer LM
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Iyer LM , Bateman A
Number in seed: 34
Number in full: 1342
Average length of the domain: 46.30 aa
Average identity of full alignment: 52 %
Average coverage of the sequence by the domain: 14.12 %

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 23.5 23.5
Trusted cut-off 23.7 23.7
Noise cut-off 23.3 23.4
Model length: 48
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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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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Tree controls

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The tree shows the occurrence of this domain across different species. More...

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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
A0A0P0XDH4 View 3D Structure Click here
A0A0R0FEJ5 View 3D Structure Click here
A0A0R0KWS7 View 3D Structure Click here
A0A0R0LIG2 View 3D Structure Click here
A0A1D6H7X4 View 3D Structure Click here
A0A368UGS1 View 3D Structure Click here
B0LUR5 View 3D Structure Click here
B0LUS5 View 3D Structure Click here
B4F9J0 View 3D Structure Click here
B4FD07 View 3D Structure Click here
B4FJE7 View 3D Structure Click here
B4FZP1 View 3D Structure Click here
B6U600 View 3D Structure Click here
C0PD69 View 3D Structure Click here
C0PNK3 View 3D Structure Click here
C4J9B4 View 3D Structure Click here
C6TKE5 View 3D Structure Click here
I1JP03 View 3D Structure Click here
I1JUN2 View 3D Structure Click here
I1L1G0 View 3D Structure Click here
I1L8A8 View 3D Structure Click here
I1LHB2 View 3D Structure Click here
I1LVK7 View 3D Structure Click here
I1M9T5 View 3D Structure Click here
I1MH56 View 3D Structure Click here
K7MNM6 View 3D Structure Click here
K7TNB0 View 3D Structure Click here
K7TVL8 View 3D Structure Click here
O04336 View 3D Structure Click here
O22176 View 3D Structure Click here
Q0JEE2 View 3D Structure Click here
Q2QMN4 View 3D Structure Click here
Q32SG4 View 3D Structure Click here
Q6K4Y7 View 3D Structure Click here
Q75KW2 View 3D Structure Click here
Q7XNY3 View 3D Structure Click here
Q93WU6 View 3D Structure Click here
Q9SJA8 View 3D Structure Click here
Q9SR07 View 3D Structure Click here
Q9STX0 View 3D Structure Click here
Q9SV15 View 3D Structure Click here

Family Structural Model

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;