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Family: zf-RING_UBOX (PF13445)

Summary: RING-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.

RING-type zinc-finger Provide feedback

This zinc-finger is a typical RING-type of plant ubiquitin ligases [1].

Literature references

  1. Stone SL, Hauksdottir H, Troy A, Herschleb J, Kraft E, Callis J;, Plant Physiol. 2005;137:13-30.: Functional analysis of the RING-type ubiquitin ligase family of Arabidopsis. PUBMED:15644464 EPMC:15644464


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR027370

This zinc-finger is the dimerisation motif for LisH proteins [ PUBMED:16445939 ]. This domain can also be found in the typical RING-type of plant ubiquitin ligases [ PUBMED:15644464 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

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
(484)
Full
(0)
Representative proteomes UniProt
(37636)
RP15
(4470)
RP35
(9466)
RP55
(19305)
RP75
(25445)
Jalview 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
(484)
Full
(0)
Representative proteomes UniProt
(37636)
RP15
(4470)
RP35
(9466)
RP55
(19305)
RP75
(25445)
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
(484)
Full
(0)
Representative proteomes UniProt
(37636)
RP15
(4470)
RP35
(9466)
RP55
(19305)
RP75
(25445)
Raw Stockholm Download     Download   Download   Download   Download   Download  
Gzipped 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_49 (release 24.0)
Previous IDs: zf-RING_LisH;
Type: Domain
Sequence Ontology: SO:0000417
Author: Wood V , Coggill P
Number in seed: 484
Number in full: 0
Average length of the domain: 0.00 aa
Average identity of full alignment: 0 %
Average coverage of the sequence by the domain: 0.00 %

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 25.2 18.0
Trusted cut-off 25.2 18.0
Noise cut-off 25.1 17.9
Model length: 40
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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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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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
A0A0G2JWJ3 View 3D Structure Click here
A0A0G2JXY7 View 3D Structure Click here
A0A0G2K313 View 3D Structure Click here
A0A0G2K6C7 View 3D Structure Click here
A0A0G2K884 View 3D Structure Click here
A0A0H2UKH6 View 3D Structure Click here
A0A0N4SU11 View 3D Structure Click here
A0A0P0XGM3 View 3D Structure Click here
A0A0R0I510 View 3D Structure Click here
A0A0R0L450 View 3D Structure Click here
A0A0R4IB88 View 3D Structure Click here
A0A0R4IBN3 View 3D Structure Click here
A0A0R4IBP6 View 3D Structure Click here
A0A0R4IBT4 View 3D Structure Click here
A0A0R4ICD1 View 3D Structure Click here
A0A0R4IEH8 View 3D Structure Click here
A0A0R4IFW2 View 3D Structure Click here
A0A0R4IIJ3 View 3D Structure Click here
A0A0R4IIL0 View 3D Structure Click here
A0A0R4IL07 View 3D Structure Click here
A0A0R4IL45 View 3D Structure Click here
A0A0R4IPB1 View 3D Structure Click here
A0A0R4IPI6 View 3D Structure Click here
A0A0R4IQ29 View 3D Structure Click here
A0A0R4ISE2 View 3D Structure Click here
A0A0R4IUT0 View 3D Structure Click here
A0A0R4IVY0 View 3D Structure Click here
A0A0R4IZN1 View 3D Structure Click here
A0A140LGW2 View 3D Structure Click here
A0A1D5NS95 View 3D Structure Click here
A0A1D5NSF2 View 3D Structure Click here
A0A1D6ENS7 View 3D Structure Click here
A0A1D6FGF6 View 3D Structure Click here
A0A1D6FWL4 View 3D Structure Click here
A0A1D6HX03 View 3D Structure Click here
A0A1D6IJX7 View 3D Structure Click here
A0A1D6KES8 View 3D Structure Click here
A0A1D6KZD4 View 3D Structure Click here
A0A1D6LIP4 View 3D Structure Click here
A0A1D6M7Z6 View 3D Structure Click here