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30  structures 420  species 0  interactions 11008  sequences 885  architectures

Family: zf-H2C2_5 (PF13909)

Summary: C2H2-type zinc-finger 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.

C2H2-type zinc-finger domain Provide feedback

No Pfam abstract.

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
(23)
Full
(11008)
Representative proteomes UniProt
(19375)
RP15
(5631)
RP35
(6987)
RP55
(11204)
RP75
(13005)
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
(23)
Full
(11008)
Representative proteomes UniProt
(19375)
RP15
(5631)
RP35
(6987)
RP55
(11204)
RP75
(13005)
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
(23)
Full
(11008)
Representative proteomes UniProt
(19375)
RP15
(5631)
RP35
(6987)
RP55
(11204)
RP75
(13005)
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:Q6IQ32
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 23
Number in full: 11008
Average length of the domain: 25.00 aa
Average identity of full alignment: 42 %
Average coverage of the sequence by the domain: 5.05 %

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 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 25
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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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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-H2C2_5 domain has been found. There are 30 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
A0A0G2JVD5 View 3D Structure Click here
A0A0G2K242 View 3D Structure Click here
A0A0G2KXF2 View 3D Structure Click here
A0A0G2KXF2 View 3D Structure Click here
A0A0R4IA51 View 3D Structure Click here
A0A0R4IM01 View 3D Structure Click here
A0A1W2Q6E1 View 3D Structure Click here
A0A1W2Q6E1 View 3D Structure Click here
A0A2R8QUZ1 View 3D Structure Click here
A0A486WWJ9 View 3D Structure Click here
A2A5K6 View 3D Structure Click here
A2ANX9 View 3D Structure Click here
A5PMB0 View 3D Structure Click here
B1AWL2 View 3D Structure Click here
B2RRE4 View 3D Structure Click here
B8JJZ4 View 3D Structure Click here
B8JJZ4 View 3D Structure Click here
D3ZFG7 View 3D Structure Click here
D3ZHB2 View 3D Structure Click here
D3ZJS6 View 3D Structure Click here
D3ZLP0 View 3D Structure Click here
D3ZQ48 View 3D Structure Click here
D3ZTY1 View 3D Structure Click here
D4ABC6 View 3D Structure Click here
E9Q8X5 View 3D Structure Click here
E9QCQ3 View 3D Structure Click here
G3V893 View 3D Structure Click here
G5E869 View 3D Structure Click here
O15090 View 3D Structure Click here
O54963 View 3D Structure Click here
P08048 View 3D Structure Click here
P17010 View 3D Structure Click here
P49711 View 3D Structure Click here
P52746 View 3D Structure Click here
Q13127 View 3D Structure Click here
Q19418 View 3D Structure Click here
Q1LUJ6 View 3D Structure Click here
Q2EI20 View 3D Structure Click here
Q5U2X9 View 3D Structure Click here
Q5U2X9 View 3D Structure Click here
Q61164 View 3D Structure Click here
Q7TS63 View 3D Structure Click here
Q7TS63 View 3D Structure Click here
Q7TSH3 View 3D Structure Click here
Q867Z4 View 3D Structure Click here
Q86UZ6 View 3D Structure Click here
Q8BID6 View 3D Structure Click here
Q8CII0 View 3D Structure Click here
Q8K083 View 3D Structure Click here
Q8NAP8 View 3D Structure Click here
Q8VIG1 View 3D Structure Click here
Q92618 View 3D Structure Click here
Q92766 View 3D Structure Click here
Q96DT7 View 3D Structure Click here
Q99KE8 View 3D Structure Click here
Q9H4Z2 View 3D Structure Click here
Q9NTW7 View 3D Structure Click here
Q9P243 View 3D Structure Click here
Q9P243 View 3D Structure Click here
Q9R1D1 View 3D Structure Click here
Q9U235 View 3D Structure Click here
Q9VPQ6 View 3D Structure Click here
Q9VPQ6 View 3D Structure Click here
Q9WTY8 View 3D Structure Click here
Q9Y462 View 3D Structure Click here
R4GDS0 View 3D Structure Click here
X1WBC8 View 3D Structure Click here
X1WBC8 View 3D Structure Click here