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0  structures 326  species 0  interactions 815  sequences 13  architectures

Family: EXS (PF03124)

Summary: EXS family

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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.

EXS family Provide feedback

We have named this region the EXS family after (ERD1, XPR1, and SYG1). This family includes C-terminus portions from the SYG1 G-protein associated signal transduction protein from Saccharomyces cerevisiae, and sequences that are thought to be murine leukaemia virus (MLV) receptors (XPR1). N-terminus portions from these proteins are aligned in the SPX PF03105 family. The previously noted similarity between SYG1 and MLV receptors over their whole sequences [1] is thus borne out in PF03105 and this family. While the N-termini aligned in PF03105 are thought to be involved in signal transduction, the role of the C-terminus sequences aligned in this family is not known. This region of similarity contains several predicted transmembrane helices. This family also includes the ERD1 (ERD: ER retention defective) yeast proteins P16151. ERD1 proteins are involved in the localisation of endogenous endoplasmic reticulum (ER) proteins. erd1 null mutants secrete such proteins even though they possess the C-terminal HDEL ER lumen localisation label sequence. In addition, null mutants also exhibit defects in the Golgi-dependent processing of several glycoproteins, which led to the suggestion that the sorting of luminal ER proteins actually occurs in the Golgi, with subsequent return of these proteins to the ER via `salvage' vesicles [2].

Literature references

  1. Battini JL, Rasko JE, Miller AD; , Proc Natl Acad Sci U S A 1999;96:1385-1390.: A human cell-surface receptor for xenotropic and polytropic murine leukemia viruses: possible role in G protein-coupled signal transduction. PUBMED:9990033 EPMC:9990033

  2. Hardwick KG, Lewis MJ, Semenza J, Dean N, Pelham HR; , EMBO J 1990;9:623-630.: ERD1, a yeast gene required for the retention of luminal endoplasmic reticulum proteins, affects glycoprotein processing in the Golgi apparatus. PUBMED:2178921 EPMC:2178921


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004342

The EXS domain is named after ERD1/XPR1/SYG1 and proteins containing this motif include the C-terminal of the SYG1 G-protein associated signal transduction protein from Saccharomyces cerevisiae, and sequences that are thought to be Murine leukemia virus (MLV) receptors (XPR1. The N-terminal of these proteins often have an SPX domain (INTERPRO) [PUBMED:9990033].

While the N-terminal is thought to be involved in signal transduction, the role of the C-terminal is not known. This region of similarity contains several predicted transmembrane helices. This family also includes the ERD1 (ERD: ER retention defective) S. cerevisiae proteins. ERD1 proteins are involved in the localization of endogenous endoplasmic reticulum (ER) proteins. Erd1 null mutants secrete such proteins even though they possess the C-terminal HDEL ER lumen localization label sequence. In addition, null mutants also exhibit defects in the Golgi-dependent processing of several glycoproteins, which led to the suggestion that the sorting of luminal ER proteins actually occurs in the Golgi, with subsequent return of these proteins to the ER via `salvage' vesicles [PUBMED:2178921].

Gene Ontology

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

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...

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
(68)
Full
(815)
Representative proteomes NCBI
(823)
Meta
(12)
RP15
(185)
RP35
(336)
RP55
(476)
RP75
(551)
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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
(68)
Full
(815)
Representative proteomes NCBI
(823)
Meta
(12)
RP15
(185)
RP35
(336)
RP55
(476)
RP75
(551)
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
(68)
Full
(815)
Representative proteomes NCBI
(823)
Meta
(12)
RP15
(185)
RP35
(336)
RP55
(476)
RP75
(551)
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.

Pfam alignments:

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_605 (release 6.5)
Previous IDs: none
Type: Family
Author: Mifsud W
Number in seed: 68
Number in full: 815
Average length of the domain: 287.00 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 50.36 %

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 25.0 25.0
Trusted cut-off 26.3 25.1
Noise cut-off 23.0 23.1
Model length: 346
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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