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1508  structures 3908  species 0  interactions 108878  sequences 1613  architectures

Family: Ion_trans (PF00520)

Summary: Ion transport protein

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Ion channel family". More...

Ion channel family Edit Wikipedia article

  • From a page move: This is a redirect from a page that has been moved (renamed). This page was kept as a redirect to avoid breaking links, both internal and external, that may have been made to the old page name.

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Ion transport protein Provide feedback

This family contains sodium, potassium and calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005821

This domain is found in sodium, potassium, and calcium ion channels proteins. The proteins have 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some Na channel proteins the domain is repeated four times, whereas in others (e.g. K channels) the protein forms a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not included in the Pfam family due to it lacking the first four helices.

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 Ion_channel (CL0030), which has the following description:

This superfamily contains a diverse range of ion channels that share a pair of transmembrane helices in common. This clan is classified as the VIC (Voltage-gated Ion Channel) superfamily in TCDB.

The clan contains the following 7 members:

Ion_trans Ion_trans_2 IRK KdpA Lig_chan PKD_channel TrkH

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
(243)
Full
(108878)
Representative proteomes UniProt
(253355)
RP15
(16966)
RP35
(41064)
RP55
(92504)
RP75
(128680)
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
(243)
Full
(108878)
Representative proteomes UniProt
(253355)
RP15
(16966)
RP35
(41064)
RP55
(92504)
RP75
(128680)
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
(243)
Full
(108878)
Representative proteomes UniProt
(253355)
RP15
(16966)
RP35
(41064)
RP55
(92504)
RP75
(128680)
Raw Stockholm Download     Download   Download   Download      
Gzipped 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_33 (release 1.0)
Previous IDs: ion_trans;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Eberhardt R
Number in seed: 243
Number in full: 108878
Average length of the domain: 245.60 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 35.89 %

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 25.0 25.0
Trusted cut-off 25.0 25.0
Noise cut-off 24.9 24.9
Model length: 245
Family (HMM) version: 33
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
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 Ion_trans domain has been found. There are 1508 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
A0A0G2K149 View 3D Structure Click here
A0A0G2K260 View 3D Structure Click here
A0A0G2K2F0 View 3D Structure Click here
A0A0G2KJE9 View 3D Structure Click here
A0A0G2KKD9 View 3D Structure Click here
A0A0G2KME3 View 3D Structure Click here
A0A0G2KRM1 View 3D Structure Click here
A0A0G2KWQ6 View 3D Structure Click here
A0A0G2KYI1 View 3D Structure Click here
A0A0G2KYI1 View 3D Structure Click here
A0A0G2KYI1 View 3D Structure Click here
A0A0G2KYI1 View 3D Structure Click here
A0A0K3AVF4 View 3D Structure Click here
A0A0P0V919 View 3D Structure Click here
A0A0P0VM15 View 3D Structure Click here
A0A0P0WX94 View 3D Structure Click here
A0A0P0XDG1 View 3D Structure Click here
A0A0P0Y7D7 View 3D Structure Click here
A0A0R0F3C0 View 3D Structure Click here
A0A0R0GLN2 View 3D Structure Click here
A0A0R0IJN5 View 3D Structure Click here
A0A0R0JZ95 View 3D Structure Click here
A0A0R4I9E2 View 3D Structure Click here
A0A0R4I9E2 View 3D Structure Click here
A0A0R4I9E2 View 3D Structure Click here
A0A0R4IDH2 View 3D Structure Click here
A0A0R4IDH2 View 3D Structure Click here
A0A0R4IDH2 View 3D Structure Click here
A0A0R4IDH2 View 3D Structure Click here
A0A0R4IEI6 View 3D Structure Click here
A0A0R4IFN9 View 3D Structure Click here
A0A0R4IFN9 View 3D Structure Click here
A0A0R4IFN9 View 3D Structure Click here
A0A0R4IFN9 View 3D Structure Click here
A0A0R4IH08 View 3D Structure Click here
A0A0R4IM91 View 3D Structure Click here
A0A0R4IMY7 View 3D Structure Click here
A0A0R4IQX8 View 3D Structure Click here
A0A0R4IQX8 View 3D Structure Click here
A0A0R4IQX8 View 3D Structure Click here
A0A0R4IQX8 View 3D Structure Click here
A0A0R4IRW0 View 3D Structure Click here
A0A0R4ISF6 View 3D Structure Click here
A0A0R4IUM7 View 3D Structure Click here
A0A0R4IUM7 View 3D Structure Click here
A0A0R4IUM7 View 3D Structure Click here
A0A0R4IUM7 View 3D Structure Click here
A0A0R4IVV4 View 3D Structure Click here
A0A0R4IVV4 View 3D Structure Click here
A0A0R4J5I1 View 3D Structure Click here
A0A140LFR8 View 3D Structure Click here
A0A142J9E8 View 3D Structure Click here
A0A1D6DWK0 View 3D Structure Click here
A0A1D6E9S9 View 3D Structure Click here
A0A1D6F9Z9 View 3D Structure Click here
A0A1D6FPS5 View 3D Structure Click here
A0A1D6FPS6 View 3D Structure Click here
A0A1D6G1L4 View 3D Structure Click here
A0A1D6G1L4 View 3D Structure Click here
A0A1D6G1L4 View 3D Structure Click here
A0A1D6G3C8 View 3D Structure Click here
A0A1D6G3D1 View 3D Structure Click here
A0A1D6GA20 View 3D Structure Click here
A0A1D6GBD0 View 3D Structure Click here
A0A1D6GGS2 View 3D Structure Click here
A0A1D6GLI0 View 3D Structure Click here
A0A1D6H5P9 View 3D Structure Click here
A0A1D6HBJ8 View 3D Structure Click here
A0A1D6HDM2 View 3D Structure Click here
A0A1D6HLR5 View 3D Structure Click here
A0A1D6HMV9 View 3D Structure Click here
A0A1D6HTC3 View 3D Structure Click here
A0A1D6HTC3 View 3D Structure Click here
A0A1D6IAL4 View 3D Structure Click here
A0A1D6L5B4 View 3D Structure Click here
A0A1D6LTF1 View 3D Structure Click here
A0A1D6LW77 View 3D Structure Click here
A0A1D6M4T0 View 3D Structure Click here
A0A1D6MG59 View 3D Structure Click here
A0A1D6MVG1 View 3D Structure Click here
A0A1D6NHI0 View 3D Structure Click here
A0A1D6NTG0 View 3D Structure Click here
A0A1D6QP96 View 3D Structure Click here
A0A1D6QPB0 View 3D Structure Click here
A0A1D6QPH6 View 3D Structure Click here
A0A286Y962 View 3D Structure Click here
A0A2R8PX35 View 3D Structure Click here
A0A2R8Q0S5 View 3D Structure Click here
A0A2R8Q672 View 3D Structure Click here
A0A2R8Q685 View 3D Structure Click here
A0A2R8Q6I1 View 3D Structure Click here
A0A2R8Q8A5 View 3D Structure Click here
A0A2R8QAI6 View 3D Structure Click here
A0A2R8QAM9 View 3D Structure Click here
A0A2R8QD79 View 3D Structure Click here
A0A2R8QEW3 View 3D Structure Click here
A0A2R8QGH1 View 3D Structure Click here
A0A2R8QHJ9 View 3D Structure Click here
A0A2R8QI74 View 3D Structure Click here
A0A2R8QJW8 View 3D Structure Click here
A0A2R8QLY1 View 3D Structure Click here
A0A2R8QLY1 View 3D Structure Click here
A0A2R8QLY1 View 3D Structure Click here
A0A2R8QLY1 View 3D Structure Click here
A0A2R8QRD4 View 3D Structure Click here
A0A2R8QRD5 View 3D Structure Click here
A0A2R8QRZ7 View 3D Structure Click here
A0A2R8QTB3 View 3D Structure Click here
A0A2R8RKE8 View 3D Structure Click here
A0A2R8RVZ4 View 3D Structure Click here
A0A2R8RYT2 View 3D Structure Click here
A0A2R8RZU5 View 3D Structure Click here
A0A3B1E007 View 3D Structure Click here
A0A3B1E663 View 3D Structure Click here
A0A3B1E663 View 3D Structure Click here
A0A3B1E663 View 3D Structure Click here
A0A3B1E663 View 3D Structure Click here
A0A4V0INI0 View 3D Structure Click here
A0JMD4 View 3D Structure Click here
A0JMD4 View 3D Structure Click here
A1Z856 View 3D Structure Click here
A1Z9N7 View 3D Structure Click here
A1ZB14 View 3D Structure Click here
A2A5F7 View 3D Structure Click here
A2APX8 View 3D Structure Click here
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A2APX8 View 3D Structure Click here
A2APX8 View 3D Structure Click here
A2ARP9 View 3D Structure Click here
A2ASI5 View 3D Structure Click here
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A2ASI5 View 3D Structure Click here
A2ASI5 View 3D Structure Click here
A2BDX4 View 3D Structure Click here
A2BG42 View 3D Structure Click here
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A2BHF4 View 3D Structure Click here
A2BHF4 View 3D Structure Click here
A2BHF4 View 3D Structure Click here
A2BHF4 View 3D Structure Click here
A2BHL7 View 3D Structure Click here
A2BHL7 View 3D Structure Click here
A2ZX97 View 3D Structure Click here
A3B9H5 View 3D Structure Click here
A3KQM6 View 3D Structure Click here
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A4HXM2 View 3D Structure Click here
A4HXM2 View 3D Structure Click here
A4HXM2 View 3D Structure Click here
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A4I9L8 View 3D Structure Click here
A6H8H5 View 3D Structure Click here
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A8B6E8 View 3D Structure Click here
A8B6E8 View 3D Structure Click here
A8DYE2 View 3D Structure Click here
A8DYR5 View 3D Structure Click here
A8JUW5 View 3D Structure Click here
A8JUW5 View 3D Structure Click here
A8JUW5 View 3D Structure Click here
A8JUW5 View 3D Structure Click here
A8MYU2 View 3D Structure Click here
A8WG04 View 3D Structure Click here
A8WHX9 View 3D Structure Click here
A9JTD2 View 3D Structure Click here
B0R0K2 View 3D Structure Click here
B0UYF4 View 3D Structure Click here
B0V138 View 3D Structure Click here
B0V2U3 View 3D Structure Click here
B1AWN6 View 3D Structure Click here
B1AWN6 View 3D Structure Click here
B1AWN6 View 3D Structure Click here
B1AWN6 View 3D Structure Click here
B1AYL1 View 3D Structure Click here
B1AYL1 View 3D Structure Click here
B1AYL1 View 3D Structure Click here
B1AYL1 View 3D Structure Click here
B2RQA1 View 3D Structure Click here
B3DHM0 View 3D Structure Click here
B3DI29 View 3D Structure Click here
B3DJ89 View 3D Structure Click here
B3DJX4 View 3D Structure Click here
B6RTA2 View 3D Structure Click here
B8JHY6 View 3D Structure Click here
B8JIR6 View 3D Structure Click here
B9F3N3 View 3D Structure Click here
B9GD29 View 3D Structure Click here
C0LU14 View 3D Structure Click here
C0LU14 View 3D Structure Click here
C0LU14 View 3D Structure Click here
C0LU14 View 3D Structure Click here
C0PDL6 View 3D Structure Click here
C4IXV6 View 3D Structure Click here
C4IXV6 View 3D Structure Click here
D3ZIU8 View 3D Structure Click here
D3ZRW4 View 3D Structure Click here
D3ZTJ6 View 3D Structure Click here
D3ZTJ6 View 3D Structure Click here
D3ZYK3 View 3D Structure Click here
D3ZZR6 View 3D Structure Click here
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D4A810 View 3D Structure Click here
D4AD53 View 3D Structure Click here
D4AD66 View 3D Structure Click here
D4ADC8 View 3D Structure Click here
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E0R7P5 View 3D Structure Click here
E0R7P9 View 3D Structure Click here
E1AZA5 View 3D Structure Click here
E1AZA6 View 3D Structure Click here
E7EEJ8 View 3D Structure Click here
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E7F278 View 3D Structure Click here
E7F278 View 3D Structure Click here
E7F278 View 3D Structure Click here
E7F278 View 3D Structure Click here
E7F3Z3 View 3D Structure Click here
E7F485 View 3D Structure Click here
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E7F8M2 View 3D Structure Click here
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E7FB36 View 3D Structure Click here
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E7FEJ3 View 3D Structure Click here
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E7FFQ6 View 3D Structure Click here
E7FGL3 View 3D Structure Click here
E9PTA2 View 3D Structure Click here
E9PU00 View 3D Structure Click here
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E9QBG4 View 3D Structure Click here
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E9QJF6 View 3D Structure Click here
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F1LMD7 View 3D Structure Click here
F1LN45 View 3D Structure Click here
F1LQF7 View 3D Structure Click here
F1LQQ7 View 3D Structure Click here
F1LQQ7 View 3D Structure Click here
F1LQQ7 View 3D Structure Click here
F1LQQ7 View 3D Structure Click here
F1LS43 View 3D Structure Click here
F1LVV2 View 3D Structure Click here
F1LY25 View 3D Structure Click here
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F1M7G0 View 3D Structure Click here
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F1Q6N3 View 3D Structure Click here
F1Q929 View 3D Structure Click here
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F1QCP2 View 3D Structure Click here
F1QCP2 View 3D Structure Click here
F1QCP2 View 3D Structure Click here
F1QCP2 View 3D Structure Click here
F1QDU6 View 3D Structure Click here
F1QG29 View 3D Structure Click here
F1QH36 View 3D Structure Click here
F1QH36 View 3D Structure Click here
F1QH36 View 3D Structure Click here
F1QH36 View 3D Structure Click here
F1QMW6 View 3D Structure Click here
F1QNK9 View 3D Structure Click here
F1QTF5 View 3D Structure Click here
F1QTV6 View 3D Structure Click here
F1QXF5 View 3D Structure Click here
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F1QXF5 View 3D Structure Click here
F1QYX6 View 3D Structure Click here
F1QZV9 View 3D Structure Click here
F1R2G3 View 3D Structure Click here
F1R3Q5 View 3D Structure Click here
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F1R736 View 3D Structure Click here
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F1R736 View 3D Structure Click here
F1R7R6 View 3D Structure Click here
F1R8I6 View 3D Structure Click here
F1RB62 View 3D Structure Click here
F1RBF8 View 3D Structure Click here
F1RC25 View 3D Structure Click here
F1RE25 View 3D Structure Click here
F1RE76 View 3D Structure Click here
F1RE76 View 3D Structure Click here
F1RE76 View 3D Structure Click here
F1RE76 View 3D Structure Click here
F6NQL8 View 3D Structure Click here
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G5EC00 View 3D Structure Click here
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I1K949 View 3D Structure Click here
I1K951 View 3D Structure Click here
I1KAP5 View 3D Structure Click here
I1KCH9 View 3D Structure Click here
I1KDG7 View 3D Structure Click here
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I1LR46 View 3D Structure Click here
I1LT39 View 3D Structure Click here
I1LTK6 View 3D Structure Click here
I1LUV8 View 3D Structure Click here
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I1M9L1 View 3D Structure Click here
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I1MF38 View 3D Structure Click here
I1MQM1 View 3D Structure Click here
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I1MUD0 View 3D Structure Click here
I1MWP6 View 3D Structure Click here
I1N4H5 View 3D Structure Click here
I1NCK8 View 3D Structure Click here
I3IS25 View 3D Structure Click here
I3ITL7 View 3D Structure Click here
J3K003 View 3D Structure Click here
J9S314 View 3D Structure Click here
K7KAI6 View 3D Structure Click here
K7KIL1 View 3D Structure Click here
K7KIP4 View 3D Structure Click here
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K7KRD9 View 3D Structure Click here
K7KTM8 View 3D Structure Click here
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K7M132 View 3D Structure Click here
K7M362 View 3D Structure Click here
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K7VQ87 View 3D Structure Click here
M0RB82 View 3D Structure Click here
M9NEI3 View 3D Structure Click here
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O00555 View 3D Structure Click here
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O35119 View 3D Structure Click here
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O35219 View 3D Structure Click here
O35433 View 3D Structure Click here
O43497 View 3D Structure Click here
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O61220 View 3D Structure Click here
O61827 View 3D Structure Click here
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