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25  structures 1575  species 0  interactions 46597  sequences 3615  architectures

Family: zf-met (PF12874)

Summary: Zinc-finger of C2H2 type

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.

Zinc-finger of C2H2 type Provide feedback

This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding.

Internal database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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
(266)
Full
(46597)
Representative proteomes UniProt
(77376)
RP15
(7428)
RP35
(17982)
RP55
(35831)
RP75
(48333)
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
(266)
Full
(46597)
Representative proteomes UniProt
(77376)
RP15
(7428)
RP35
(17982)
RP55
(35831)
RP75
(48333)
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
(266)
Full
(46597)
Representative proteomes UniProt
(77376)
RP15
(7428)
RP35
(17982)
RP55
(35831)
RP75
(48333)
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: manual
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 266
Number in full: 46597
Average length of the domain: 23.80 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 5.56 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.2 13.3
Trusted cut-off 21.2 13.3
Noise cut-off 21.1 13.2
Model length: 25
Family (HMM) version: 10
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

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.

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 zf-met domain has been found. There are 25 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
A0A0B4LFS0 View 3D Structure Click here
A0A0G2K1A1 View 3D Structure Click here
A0A0G2K4A6 View 3D Structure Click here
A0A0G2KIM8 View 3D Structure Click here
A0A0G2KM98 View 3D Structure Click here
A0A0G2L0F1 View 3D Structure Click here
A0A0G2L199 View 3D Structure Click here
A0A0G2LA56 View 3D Structure Click here
A0A0P0XDW6 View 3D Structure Click here
A0A0P0XG62 View 3D Structure Click here
A0A0P0XN80 View 3D Structure Click here
A0A0P0XVG3 View 3D Structure Click here
A0A0R0F9Y8 View 3D Structure Click here
A0A0R0FEN1 View 3D Structure Click here
A0A0R0FEN8 View 3D Structure Click here
A0A0R0FF65 View 3D Structure Click here
A0A0R0FFE3 View 3D Structure Click here
A0A0R0FJ84 View 3D Structure Click here
A0A0R0G344 View 3D Structure Click here
A0A0R0KED3 View 3D Structure Click here
A0A0R0KNJ7 View 3D Structure Click here
A0A0R0L3Y3 View 3D Structure Click here
A0A0R0LAV8 View 3D Structure Click here
A0A0R4IQP3 View 3D Structure Click here
A0A0R4IVQ9 View 3D Structure Click here
A0A1D6EQ20 View 3D Structure Click here
A0A1D6EUS5 View 3D Structure Click here
A0A1D6F9D3 View 3D Structure Click here
A0A1D6GUE1 View 3D Structure Click here
A0A1D6I4I6 View 3D Structure Click here
A0A1D6I4I8 View 3D Structure Click here
A0A1D6JR73 View 3D Structure Click here
A0A1D6K8J5 View 3D Structure Click here
A0A1D6MER1 View 3D Structure Click here
A0A1D6MI97 View 3D Structure Click here
A0A1D6P6Y6 View 3D Structure Click here
A0A1D6Q058 View 3D Structure Click here
A0A1D8PGM6 View 3D Structure Click here
A0A1D8PIC1 View 3D Structure Click here
A0A1D8PNA1 View 3D Structure Click here