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.
0  structures 115  species 0  interactions 193  sequences 6  architectures

Family: GLTSCR1 (PF15249)

Summary: Glioma tumor suppressor candidate region

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

Ion channel (eukaryotic)
2r9r opm.png
Potassium channel Kv1.2 (with beta2 auxiliary subunits), structure in a membrane-like environment. Calculated hydrocarbon boundaries of the lipid bilayer are indicated by red and blue dots.
Identifiers
Symbol Ion_trans
Pfam PF00520
InterPro IPR005821
SCOP 1bl8
SUPERFAMILY 1bl8
TCDB 1.A.1
OPM superfamily 8
OPM protein 2a79
Ion channel (bacterial)
1r3j.png
Potassium channel KcsA. Calculated hydrocarbon boundaries of the lipid bilayer are indicated by red and blue dots.
Identifiers
Symbol Ion_trans_2
Pfam PF07885
InterPro IPR013099
SCOP 1bl8
SUPERFAMILY 1bl8
OPM protein 1r3j

Transmembrane ion channel family was defined in InterPro and Pfam as the family of tetrameric sodium, potassium, and calcium ion channels, in which two C-terminal transmembrane helices flank a loop which determines ion selectivity of the channel pore. This large group of ion channels apparently includes families 1.A.1, 1.A.2, 1.A.3, and 1.A.4 of transporter classification.

Many eukaryotic channels have four additional transmembrane helices (TMH) (Pfam PF00520), whereas a bacterial structure of the protein has only two transmembrane helices that form the tetrameric channel (Pfam PF07885).

Human channels with 6 TM helices

Cation

Calcium

Potassium[1]

Sodium

Proton

Cyclic nucleotide-gated

Human channels with two TM helices in each subunit, as in bacteria

Potassium

References

  1. ^ Choe S (February 2002). "Potassium channel structures". Nat. Rev. Neurosci. 3 (2): 115–21. doi:10.1038/nrn727. PMID 11836519. 

External links


This article incorporates text from the public domain Pfam and InterPro IPR005821

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.

Glioma tumor suppressor candidate region Provide feedback

This domain family is found in eukaryotes, and is typically between 105 and 124 amino acids in length. There is a single completely conserved residue F that may be functionally important. Mutations in the gene for this protein in humans leads to the development of oligodendrogliomas [1]. There is evidence that these protein interacts with SH3 domains [2].

Literature references

  1. Yang P, Kollmeyer TM, Buckner K, Bamlet W, Ballman KV, Jenkins RB;, Cancer. 2005;103:2363-2372.: Polymorphisms in GLTSCR1 and ERCC2 are associated with the development of oligodendrogliomas. PUBMED:15834925 EPMC:15834925

  2. Wu C, Ma MH, Brown KR, Geisler M, Li L, Tzeng E, Jia CY, Jurisica I, Li SS;, Proteomics. 2007;7:1775-1785.: Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening. PUBMED:17474147 EPMC:17474147


External database links

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...

Loading domain graphics...

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 8 members:

GLTSCR1 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 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
(54)
Full
(193)
Representative proteomes NCBI
(197)
Meta
(0)
RP15
(38)
RP35
(57)
RP55
(88)
RP75
(126)
Jalview View  View  View  View  View  View  View   
HTML View  View  View  View  View  View     
PP/heatmap 1 View  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
(54)
Full
(193)
Representative proteomes NCBI
(197)
Meta
(0)
RP15
(38)
RP35
(57)
RP55
(88)
RP75
(126)
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
(54)
Full
(193)
Representative proteomes NCBI
(197)
Meta
(0)
RP15
(38)
RP35
(57)
RP55
(88)
RP75
(126)
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.

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.

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

This family is new in this Pfam release.

Seed source: Jackhmmer:Q9NZM4
Previous IDs: none
Type: Family
Author: Eberhardt RY, Coggill P, Hetherington K
Number in seed: 54
Number in full: 193
Average length of the domain: 109.40 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 10.45 %

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 27.0 27.0
Trusted cut-off 27.6 27.4
Noise cut-off 26.9 26.6
Model length: 109
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

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.