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6  structures 1172  species 0  interactions 3634  sequences 68  architectures

Family: EBP (PF05241)

Summary: EXPERA (EXPanded EBP superfamily)

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.

EXPERA (EXPanded EBP superfamily) Provide feedback

The EXPERA (EXPanded EBP superfamily) domain is conserved among the following protein families: TM6SF1 (Transmembrane 6 Superfamily Member 1), TM6SF2 (Transmembrane 6 Superfamily Member 2), MAC30 (Meningioma-associated protein 30 also known as TMEM97, or Transmembrane protein 97), and EBP (Emopamil binding protein). EBP is an enzyme with a D8, D7 sterol isomerase activity that catalyzes the transposition of a double bond from C8=C9 to C7=C8 in the sterol B-ring. Mutations of EBP are known to cause the genetic disorder of X-linked dominant chondrodysplasia punctata (CDPX2). This syndrome of humans is lethal in most males, and affected females display asymmetric hyperkeratotic skin and skeletal abnormalities [1].

Literature references

  1. Sanchez-Pulido L, Ponting CP;, Front Genet. 2014;5:439.: TM6SF2 and MAC30, new enzyme homologs in sterol metabolism and common metabolic disease. PUBMED:25566323 EPMC:25566323


This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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 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
(683)
Full
(3634)
Representative proteomes UniProt
(5834)
RP15
(490)
RP35
(1458)
RP55
(2631)
RP75
(3817)
Jalview View  View  View  View  View  View  View 
HTML View  View           
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
(683)
Full
(3634)
Representative proteomes UniProt
(5834)
RP15
(490)
RP35
(1458)
RP55
(2631)
RP75
(3817)
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
(683)
Full
(3634)
Representative proteomes UniProt
(5834)
RP15
(490)
RP35
(1458)
RP55
(2631)
RP75
(3817)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: Pfam-B_7320 (release 7.7)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Moxon SJ
Number in seed: 683
Number in full: 3634
Average length of the domain: 111.60 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 47.12 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.7 25.7
Trusted cut-off 25.7 25.7
Noise cut-off 25.6 25.6
Model length: 115
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Viroids Viroids Unclassified sequence Unclassified sequence

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 EBP domain has been found. There are 6 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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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
A0A0G2JZS3 View 3D Structure Click here
A0A1D6HXK5 View 3D Structure Click here
A0A1D6MP14 View 3D Structure Click here
A0A1D8PQN5 View 3D Structure Click here
A0A2R8Q2C6 View 3D Structure Click here
A4HWT3 View 3D Structure Click here
B6TIR9 View 3D Structure Click here
B8A4R3 View 3D Structure Click here
D3ZXC8 View 3D Structure Click here
F1QDW6 View 3D Structure Click here
I1KFB7 View 3D Structure Click here
I1L4E2 View 3D Structure Click here
I1L4E4 View 3D Structure Click here
I1L4E5 View 3D Structure Click here
I1LRR4 View 3D Structure Click here
K7LX60 View 3D Structure Click here
O23046 View 3D Structure Click here
O23047 View 3D Structure Click here
O48962 View 3D Structure Click here
P58749 View 3D Structure Click here
P70245 View 3D Structure Click here
Q10255 View 3D Structure Click here
Q10G23 View 3D Structure Click here
Q12155 View 3D Structure Click here
Q15125 View 3D Structure Click here
Q4CX37 View 3D Structure Click here
Q4DPN5 View 3D Structure Click here
Q55E32 View 3D Structure Click here
Q5BJF2 View 3D Structure Click here
Q5U3Y7 View 3D Structure Click here
Q84YQ4 View 3D Structure Click here
Q84YQ5 View 3D Structure Click here
Q8VD00 View 3D Structure Click here
Q9BY08 View 3D Structure Click here
Q9BZW5 View 3D Structure Click here
Q9D0P0 View 3D Structure Click here
Q9FTZ2 View 3D Structure Click here
Q9JJ46 View 3D Structure Click here
Q9ZV66 View 3D Structure Click here