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10  structures 4824  species 0  interactions 12806  sequences 54  architectures

Family: Cation_efflux (PF01545)

Summary: Cation efflux family

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.

Cation efflux family Provide feedback

Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are thought to be efflux pumps that remove these ions from cells.

Literature references

  1. Xiong A, Jayaswal RK; , J Bacteriol 1998;180:4024-4029.: Molecular characterization of a chromosomal determinant conferring resistance to zinc and cobalt ions in Staphylococcus aureus. PUBMED:9696746 EPMC:9696746

  2. Kunito T, Kusano T, Oyaizu H, Senoo K, Kanazawa S, Matsumoto S; , Biosci Biotechnol Biochem 1996;60:699-704.: Cloning and sequence analysis of czc genes in Alcaligenes sp. strain CT14. PUBMED:8829543 EPMC:8829543


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002524

Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are considered to be efflux pumps that remove these ions from cells [PUBMED:9696746, PUBMED:8829543], however others are implicated in ion uptake [PUBMED:1508175]. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence.

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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Pfam Clan

This family is a member of clan DMT (CL0184), which has the following description:

This clan contains a variety of transporters which have 4, 5, 9 or 10 membrane spanning helices. Many of the 10 membrane spanning transporters appear to be a duplication of the 5 spanning unit [1]. Many of these families contain a characteristic glycine rich motif close to the C-terminus.

The clan contains the following 20 members:

Cation_efflux CRCB CRT-like DUF1632 DUF486 DUF606 DUF914 EamA EmrE Mg_trans_NIPA Multi_Drug_Res Nuc_sug_transp RhaT Sugar_transport TPT UAA UPF0060 UPF0546 Ureide_permease Zip

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
(89)
Full
(12806)
Representative proteomes NCBI
(10055)
Meta
(1117)
RP15
(1327)
RP35
(2487)
RP55
(3430)
RP75
(4122)
Jalview View  View  View  View  View  View  View  View 
HTML View    View  View  View  View     
PP/heatmap 1   View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(89)
Full
(12806)
Representative proteomes NCBI
(10055)
Meta
(1117)
RP15
(1327)
RP35
(2487)
RP55
(3430)
RP75
(4122)
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
(89)
Full
(12806)
Representative proteomes NCBI
(10055)
Meta
(1117)
RP15
(1327)
RP35
(2487)
RP55
(3430)
RP75
(4122)
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_232 (release 4.0)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 89
Number in full: 12806
Average length of the domain: 268.50 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 81.33 %

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 22.8 22.8
Trusted cut-off 22.8 22.9
Noise cut-off 22.7 22.7
Model length: 285
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

Sunburst controls

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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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Tree controls

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The tree shows the occurrence of this domain across different species. 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 Cation_efflux domain has been found. There are 10 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 seqence.

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