Summary: Cation transport protein
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Cation transport protein Provide feedback
This family consists of various cation transport proteins (Trk) and V-type sodium ATP synthase subunit J or translocating ATPase J EC:3.6.1.34. These proteins are involved in active sodium up-take utilising ATP in the process. TrkH a member of the family P76769 from E. coli is a hydrophobic membrane protein and determines the specificity and kinetics of cation transport by the TrK system in E. coli [3].
Literature references
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Cziepluch C, Kordes E, Pujol A, Jauniaux JC; , Yeast 1996;12:1471-1474.: Sequencing analysis of a 40.2 kb fragment of yeast chromosome X reveals 19 open reading frames including URA2 (5' end), TRK1, PBS2, SPT10, GCD14, RPE1, PHO86, NCA3, ASF1, CCT7, GZF3, two tRNA genes, three remnant delta elements and a Ty4 transposon. PUBMED:8948101 EPMC:8948101
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Schlosser A, Meldorf M, Stumpe S, Bakker EP, Epstein W; , J Bacteriol 1995;177:1908-1910.: TrkH and its homolog, TrkG, determine the specificity and kinetics of cation transport by the Trk system of Escherichia coli. PUBMED:7896723 EPMC:7896723
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Schlosser A, Meldorf M, Stumpe S, Bakker EP, Epstein W; , J Bacteriol 1995;177:1908-1910.: TrkH and its homolog, TrkG, determine the specificity and kinetics of cation transport by the Trk system of Escherichia coli. PUBMED:7896723 EPMC:7896723
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Calero F, Gomez N, Arino J, Ramos J; , J Bacteriol 2000;182:394-399.: Trk1 and Trk2 define the major K(+) transport system in fission yeast. PUBMED:10629185 EPMC:10629185
Internal database links
SCOOP: | KdpA |
External database links
Transporter classification: | 2.A.38 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR003445
This family consists of various potassium transport proteins (Trk) and V-type sodium ATP synthase subunit J or translocating ATPase J (EC). These proteins are involved in active sodium up-take utilizing ATP in the process. TrkH from Escherichia coli is a hydrophobic membrane protein and determines the specificity and kinetics of cation transport by the TrK system in this organism [PUBMED:7896723]. This protein interacts with TrkA and requires TrkE for transport activity.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | cation transmembrane transporter activity (GO:0008324) |
Biological process | transmembrane transport (GO:0055085) |
cation transport (GO:0006812) |
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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 (9) |
Full (11017) |
Representative proteomes | UniProt (45307) |
NCBI (56856) |
Meta (4316) |
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RP15 (1384) |
RP35 (5282) |
RP55 (10268) |
RP75 (17007) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
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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 (9) |
Full (11017) |
Representative proteomes | UniProt (45307) |
NCBI (56856) |
Meta (4316) |
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RP15 (1384) |
RP35 (5282) |
RP55 (10268) |
RP75 (17007) |
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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_529 (release 5.2) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bashton M |
Number in seed: | 9 |
Number in full: | 11017 |
Average length of the domain: | 378.50 aa |
Average identity of full alignment: | 19 % |
Average coverage of the sequence by the domain: | 80.17 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 502 | ||||||||||||
Family (HMM) version: | 17 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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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Interactions
There is 1 interaction for this family. More...
TrkHStructures
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 TrkH domain has been found. There are 14 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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