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0  structures 848  species 0  interactions 14929  sequences 3031  architectures

Family: zf-C2H2_4 (PF13894)

Summary: C2H2-type zinc finger

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.

C2H2-type zinc finger Provide feedback

This family contains a number of divergent C2H2 type zinc fingers.

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
(313)
Full
(14929)
Representative proteomes UniProt
(25242)
RP15
(3058)
RP35
(6112)
RP55
(11434)
RP75
(15078)
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
(313)
Full
(14929)
Representative proteomes UniProt
(25242)
RP15
(3058)
RP35
(6112)
RP55
(11434)
RP75
(15078)
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
(313)
Full
(14929)
Representative proteomes UniProt
(25242)
RP15
(3058)
RP35
(6112)
RP55
(11434)
RP75
(15078)
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: Jackhmmer
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 313
Number in full: 14929
Average length of the domain: 24.00 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 4.97 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 19.8
Trusted cut-off 27.0 19.8
Noise cut-off 26.9 19.7
Model length: 24
Family (HMM) version: 9
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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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
A0A087WNP5 View 3D Structure Click here
A0A0G2KA26 View 3D Structure Click here
A0A0G2KAJ3 View 3D Structure Click here
A0A0G2KC74 View 3D Structure Click here
A0A0G2KC95 View 3D Structure Click here
A0A0G2KCQ2 View 3D Structure Click here
A0A0G2KFJ8 View 3D Structure Click here
A0A0G2KH00 View 3D Structure Click here
A0A0G2KIV9 View 3D Structure Click here
A0A0G2KLM8 View 3D Structure Click here
A0A0G2KLU1 View 3D Structure Click here
A0A0G2KM98 View 3D Structure Click here
A0A0G2KMM6 View 3D Structure Click here
A0A0G2KN93 View 3D Structure Click here
A0A0G2KPH2 View 3D Structure Click here
A0A0G2KQN2 View 3D Structure Click here
A0A0G2KQY5 View 3D Structure Click here
A0A0G2KYH8 View 3D Structure Click here
A0A0G2L082 View 3D Structure Click here
A0A0G2L0F1 View 3D Structure Click here
A0A0G2L0M4 View 3D Structure Click here
A0A0G2L427 View 3D Structure Click here
A0A0G2L6R0 View 3D Structure Click here
A0A0G2L8W6 View 3D Structure Click here
A0A0G2L9C4 View 3D Structure Click here
A0A0G2L9I6 View 3D Structure Click here
A0A0H2UJC5 View 3D Structure Click here
A0A0J9YJ47 View 3D Structure Click here
A0A0J9YUD4 View 3D Structure Click here
A0A0N4STY5 View 3D Structure Click here
A0A0N4SU17 View 3D Structure Click here
A0A0R0HRK1 View 3D Structure Click here
A0A0R4I9J7 View 3D Structure Click here
A0A0R4IAQ0 View 3D Structure Click here
A0A0R4IBV3 View 3D Structure Click here
A0A0R4ICG2 View 3D Structure Click here
A0A0R4ICQ4 View 3D Structure Click here
A0A0R4IDX8 View 3D Structure Click here
A0A0R4IE88 View 3D Structure Click here
A0A0R4IEP4 View 3D Structure Click here