Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
8  structures 467  species 0  interactions 8090  sequences 8  architectures

Family: Mce4_CUP1 (PF11887)

Summary: Cholesterol uptake porter CUP1 of Mce4, putative

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.

Cholesterol uptake porter CUP1 of Mce4, putative Provide feedback

Mce4_CUP1 is a family of putative Mce4 transporters of cholesterol. The domain is found associated with PF02470. The full TCDB classification for this family in conjunction with PF02470 is 3.A.1.27.4.

Literature references

  1. Mohn WW, van der Geize R, Stewart GR, Okamoto S, Liu J, Dijkhuizen L, Eltis LD;, J Biol Chem. 2008;283:35368-35374.: The actinobacterial mce4 locus encodes a steroid transporter. PUBMED:18955493 EPMC:18955493


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR024516

This entry represents a domain of unknown function found at the C terminus of many proteins in the mammalian cell entry family.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

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
(57)
Full
(8090)
Representative proteomes UniProt
(34418)
RP15
(332)
RP35
(2637)
RP55
(8994)
RP75
(17868)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(57)
Full
(8090)
Representative proteomes UniProt
(34418)
RP15
(332)
RP35
(2637)
RP55
(8994)
RP75
(17868)
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
(57)
Full
(8090)
Representative proteomes UniProt
(34418)
RP15
(332)
RP35
(2637)
RP55
(8994)
RP75
(17868)
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_3559 (release 23.0)
Previous IDs: DUF3407;
Type: Family
Sequence Ontology: SO:0100021
Author: Assefa S , Coggill P , Bateman A
Number in seed: 57
Number in full: 8090
Average length of the domain: 206 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 52.4 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 32.6 32.6
Trusted cut-off 32.6 32.6
Noise cut-off 32.5 32.5
Model length: 221
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 Mce4_CUP1 domain has been found. There are 8 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.

Loading structure mapping...

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
I6WYT7 View 3D Structure Click here
I6X7G8 View 3D Structure Click here
I6XHD6 View 3D Structure Click here
I6Y461 View 3D Structure Click here
I6YC99 View 3D Structure Click here
K0EH07 View 3D Structure Click here
K0EIY8 View 3D Structure Click here
K0EMA5 View 3D Structure Click here
K0ENJ3 View 3D Structure Click here
K0ES52 View 3D Structure Click here
K0EUP2 View 3D Structure Click here
K0F084 View 3D Structure Click here
K0F2D7 View 3D Structure Click here
K0F763 View 3D Structure Click here
K0F7C4 View 3D Structure Click here
K0F7D6 View 3D Structure Click here
K0F7E0 View 3D Structure Click here
K0F845 View 3D Structure Click here
K0F848 View 3D Structure Click here
K0F8D1 View 3D Structure Click here
K0F9A6 View 3D Structure Click here
K0F9A9 View 3D Structure Click here
K0F9D8 View 3D Structure Click here
K0FA81 View 3D Structure Click here
K0FD54 View 3D Structure Click here
K0FDA5 View 3D Structure Click here
L0T2W6 View 3D Structure Click here
L7N698 View 3D Structure Click here
O07414 View 3D Structure Click here
O07415 View 3D Structure Click here
O07416 View 3D Structure Click here
O07784 View 3D Structure Click here
O07787 View 3D Structure Click here
O07788 View 3D Structure Click here
O53968 View 3D Structure Click here
O53969 View 3D Structure Click here
O53970 View 3D Structure Click here
O53971 View 3D Structure Click here
Q79FY7 View 3D Structure Click here
Q79FZ9 View 3D Structure Click here