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0  structures 248  species 0  interactions 412  sequences 64  architectures

Family: CLU (PF13236)

Summary: Clustered mitochondria

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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.

Clustered mitochondria Provide feedback

The CLU domain (CLUstered mitochondria) is a eukaryotic domain found in proteins from fungi, protozoa, plants to humans. It is required for correct functioning of the mitochondria and mitochondrial transport [1,2] although the exact function of the domain is unknown [4]. In Dictyostelium the full-length protein is required for a very late step in fission of the outer mitochondrial membrane [2] suggesting that mitochondria are transported along microtubules, as in mammalian cells, rather than along actin filaments, as in budding yeast [1]. Disruption of the protein-impaired cytokinesis and caused mitochondria to cluster at the cell centre [1]. It is likely that CLU functions in a novel pathway that positions mitochondria within the cell based on their physiological state. Disruption of the CLU pathway may enhance oxidative damage, alter gene expression, cause mitochondria to cluster at microtubule plus ends, and lead eventually to mitochondrial failure [3].

Literature references

  1. Zhu Q, Hulen D, Liu T, Clarke M;, Proc Natl Acad Sci U S A. 1997;94:7308-7313.: The cluA- mutant of Dictyostelium identifies a novel class of proteins required for dispersion of mitochondria. PUBMED:9207087 EPMC:9207087

  2. Fields SD, Arana Q, Heuser J, Clarke M;, J Muscle Res Cell Motil. 2002;23:829-838.: Mitochondrial membrane dynamics are altered in cluA- mutants of Dictyostelium. PUBMED:12952081 EPMC:12952081

  3. Cox RT, Spradling AC;, Dis Model Mech. 2009;2:490-499.: Clueless, a conserved Drosophila gene required for mitochondrial subcellular localization, interacts genetically with parkin. PUBMED:19638420 EPMC:19638420

  4. Sugden C, Ross S, Bloomfield G, Ivens A, Skelton J, Mueller-Taubenberger A, Williams JG;, J Biol Chem. 2010;285:22927-22935.: Two novel Src homology 2 domain proteins interact to regulate dictyostelium gene expression during growth and early development. PUBMED:20457612 EPMC:20457612


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR025697

The CLU domain (CLUstered mitochondria) is a eukaryotic domain found in highly conserved eukaryotic proteins required for correct mitochondrial dispersal [PUBMED:9207087, PUBMED:12952081]. The exact function of the domain is unknown [PUBMED:20457612].

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(42)
Full
(412)
Representative proteomes NCBI
(412)
Meta
(5)
RP15
(124)
RP35
(189)
RP55
(271)
RP75
(310)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(42)
Full
(412)
Representative proteomes NCBI
(412)
Meta
(5)
RP15
(124)
RP35
(189)
RP55
(271)
RP75
(310)
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
(42)
Full
(412)
Representative proteomes NCBI
(412)
Meta
(5)
RP15
(124)
RP35
(189)
RP55
(271)
RP75
(310)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: [1]
Previous IDs: none
Type: Domain
Author: Fey P, Coggill P
Number in seed: 42
Number in full: 412
Average length of the domain: 207.90 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 16.22 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.4 21.4
Trusted cut-off 21.6 21.5
Noise cut-off 21.3 20.9
Model length: 221
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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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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