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0  structures 559  species 0  interactions 899  sequences 11  architectures

Family: GIDE (PF12483)

Summary: E3 Ubiquitin ligase

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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.

E3 Ubiquitin ligase Provide feedback

This domain family is found in bacteria, archaea and eukaryotes, and is typically between 150 and 163 amino acids in length. There is a single completely conserved residue E that may be functionally important. GIDE is an E3 ubiquitin ligase which is involved in inducing apoptosis.

Literature references

  1. Zhang B, Huang J, Li HL, Liu T, Wang YY, Waterman P, Mao AP, Xu LG, Zhai Z, Liu D, Marrack P, Shu HB;, Cell Res. 2008;18:900-910.: GIDE is a mitochondrial E3 ubiquitin ligase that induces apoptosis and slows growth. PUBMED:18591963 EPMC:18591963


This tab holds annotation information from the InterPro database.

InterPro entry IPR022170

This family includes mitochondrial ubiquitin ligase activator of NFKB 1 (MULAN, also known as GIDE) and in ubiquitin E3 Ligase SP1.

GIDE exhibits weak E3 ubiquitin-protein ligase activity, but preferentially acts as a SUMO E3 ligase at physiological concentrations [PUBMED:18591963]. It plays a role in the control of mitochondrial morphology, promotes mitochondrial fragmentation and influences mitochondrial localisation [PUBMED:18207745]. When over-expressed in human cells, it activates JNK through MAP3K7/TAK1 and induces caspase-dependent apoptosis [PUBMED:18591963].

Ubiquitin E3 ligase SP1 associates with TOC (translocon at the outer envelope membrane of chloroplasts) complexes and mediates ubiquitination of TOC components, promoting their degradation. SP1-mediated regulation of chloroplast protein import contributes to the organellar proteome changes that occur during plant development [PUBMED:23118188]. It is also important for stress tolerance in plants [PUBMED:26387714].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(24)
Full
(899)
Representative proteomes UniProt
(1651)
NCBI
(2395)
Meta
(29)
RP15
(237)
RP35
(561)
RP55
(812)
RP75
(965)
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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
(24)
Full
(899)
Representative proteomes UniProt
(1651)
NCBI
(2395)
Meta
(29)
RP15
(237)
RP35
(561)
RP55
(812)
RP75
(965)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(24)
Full
(899)
Representative proteomes UniProt
(1651)
NCBI
(2395)
Meta
(29)
RP15
(237)
RP35
(561)
RP55
(812)
RP75
(965)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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: Prosite
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Gavin OL
Number in seed: 24
Number in full: 899
Average length of the domain: 147.40 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 45.56 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.6 23.6
Trusted cut-off 23.6 23.7
Noise cut-off 23.5 23.5
Model length: 158
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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