Summary: Inward rectifier potassium channel transmembrane domain
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This is the Wikipedia entry entitled "Inward-rectifier potassium ion channel". More...
Inward-rectifier potassium ion channel Edit Wikipedia article
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Inward rectifier potassium channel transmembrane domain Provide feedback
No Pfam abstract.
Literature references
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Doupnik CA, Davidson N, Lester HA; , Curr Opin Neurobiol 1995;5:268-277.: The inward rectifier potassium channel family. PUBMED:7580148 EPMC:7580148
Internal database links
SCOOP: | Ion_trans Ion_trans_2 |
External database links
MIM: | 601678 |
SCOP: | 1n9p |
Transporter classification: | 1.A.2 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR040445
Inwardly-rectifying potassium channels (Kir) are the principal class of two-TM domain potassium channels. They are characterised by the property of inward-rectification, which is described as the ability to allow large inward currents and smaller outward currents. Inwardly rectifying potassium channels (Kir) are responsible for regulating diverse processes including: cellular excitability, vascular tone, heart rate, renal salt flow, and insulin release [ PUBMED:10102275 ]. To date, around twenty members of this superfamily have been cloned, which can be grouped into six families by sequence similarity, and these are designated Kir1.x-6.x [ PUBMED:7580148 , PUBMED:10449331 ].
Cloned Kir channel cDNAs encode proteins of between ~370-500 residues, both N- and C-termini are thought to be cytoplasmic, and the N terminus lacks a signal sequence. Kir channel alpha subunits possess only 2TM domains linked with a P-domain. The two 'transmembrane passes' place the C-terminal tail on the cytoplasmic side of the membrane [ PUBMED:7580148 ]. It is thought that four Kir subunits assemble to form a tetrameric channel complex, which may be hetero- or homomeric [ PUBMED:10102275 ].
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 TrkHAlignments
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...
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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 (31) |
Full (5110) |
Representative proteomes | UniProt (9172) |
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RP15 (720) |
RP35 (1913) |
RP55 (4505) |
RP75 (5886) |
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Jalview | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (31) |
Full (5110) |
Representative proteomes | UniProt (9172) |
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RP15 (720) |
RP35 (1913) |
RP55 (4505) |
RP75 (5886) |
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Raw Stockholm | |||||||
Gzipped |
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
Seed source: | Pfam-B_18 (release 3.0) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 31 |
Number in full: | 5110 |
Average length of the domain: | 137.40 aa |
Average identity of full alignment: | 44 % |
Average coverage of the sequence by the domain: | 32.95 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 142 | ||||||||||||
Family (HMM) version: | 22 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 IRK domain has been found. There are 94 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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