Summary: LETM1-like protein
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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.
LETM1-like protein Provide feedback
Members of this family are inner mitochondrial membrane proteins which play a role in potassium and hydrogen ion exchange [3]. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans [1].
Literature references
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Endele S, Fuhry M, Pak SJ, Zabel BU, Winterpacht A; , Genomics 1999;60:218-225.: LETM1, a novel gene encoding a putative EF-hand Ca(2+)-binding protein, flanks the Wolf-Hirschhorn syndrome (WHS) critical region and is deleted in most WHS patients. PUBMED:10486213 EPMC:10486213
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Caggese C, Ragone G, Perrini B, Moschetti R, De Pinto V, Caizzi R, Barsanti P; , Mol Gen Genet 1999;261:64-70.: Identification of nuclear genes encoding mitochondrial proteins: isolation of a collection of D. melanogaster cDNAs homologous to sequences in the Human Gene Index database. PUBMED:10071211 EPMC:10071211
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Froschauer E, Nowikovsky K, Schweyen RJ; , Biochim Biophys Acta 2005;1711:41-48.: Electroneutral K+/H+ exchange in mitochondrial membrane vesicles involves Yol027/Letm1 proteins. PUBMED:15904662 EPMC:15904662
External database links
Transporter classification: | 8.A.20 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR011685
This is a group of mainly hypothetical eukaryotic proteins. Putative features found in LETM1, such as a transmembrane domain and a CK2 and PKC phosphorylation site [PUBMED:10486213], are relatively conserved throughout the family. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans [PUBMED:10486213]. A member of this family, SWISSPROT, is known to be expressed in the mitochondria of Drosophila melanogaster [PUBMED:10071211], suggesting that this may be a group of mitochondrial proteins.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, the UniProtKB sequence database, 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 (147) |
Full (2915) |
Representative proteomes | UniProt (4290) |
NCBI (5925) |
Meta (36) |
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RP15 (786) |
RP35 (1642) |
RP55 (2292) |
RP75 (2756) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
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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 (147) |
Full (2915) |
Representative proteomes | UniProt (4290) |
NCBI (5925) |
Meta (36) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (786) |
RP35 (1642) |
RP55 (2292) |
RP75 (2756) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Pfam-B_2202 (release 14.0) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Fenech M |
Number in seed: | 147 |
Number in full: | 2915 |
Average length of the domain: | 199.70 aa |
Average identity of full alignment: | 27 % |
Average coverage of the sequence by the domain: | 39.95 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 268 | ||||||||||||
Family (HMM) version: | 13 | ||||||||||||
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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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 LETM1 domain has been found. There are 1 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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