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3  structures 1869  species 1  interaction 2392  sequences 9  architectures

Family: Na_H_antiport_1 (PF06965)

Summary: Na+/H+ antiporter 1

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This is the Wikipedia entry entitled "Sodium/proton antiporter 1". More...

Sodium/proton antiporter 1 Edit Wikipedia article

Na+/H+ antiporter 1
1zcd opm.gif
Identifiers
Symbol Na_H_antiport_1
Pfam PF06965
InterPro IPR004670
TCDB 2.A.36
OPM superfamily 346
OPM protein 1zcd

Na+/H+ antiporter 1 family contains a number of bacterial Na+/H+ antiporter 1 proteins. These are integral membrane proteins that catalyse the exchange of H+ for Na+ in a manner that is highly dependent on the pH.

In particular, the Escherichia coli NhaA Na+:H+ Antiporter (NhaA) protein probably functions in the regulation of the internal pH when the external pH is alkaline. It also uses the H+ gradient to expel Na+ from the cell. Its activity is highly pH dependent.

References[edit]

  • Karpel, R.; Alon, T.; Glaser, G.; Schuldiner, S.; Padan, E. (1991). "Expression of a sodium proton antiporter (NhaA) in Escherichia coli is induced by Na+ and Li+ ions". The Journal of biological chemistry 266 (32): 21753–21759. PMID 1657980. 

This article incorporates text from the public domain Pfam and InterPro IPR004670


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.

Na+/H+ antiporter 1 Provide feedback

This family contains a number of bacterial Na+/H+ antiporter 1 proteins. These are integral membrane proteins that catalyse the exchange of H+ for Na+ in a manner that is highly dependent on the pH [1].

Literature references

  1. Karpel R, Alon T, Glaser G, Schuldiner S, Padan E; , J Biol Chem 1991;266:21753-21759.: Expression of a sodium proton antiporter (NhaA) in Escherichia coli is induced by Na+ and Li+ ions. PUBMED:1657980 EPMC:1657980


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004670

NhaA is a sodium ion/proton antiporter that uses the proton electrochemical gradient to expel sodium ions from the cytoplasm and functions primarily in the adaptation to high salinity at alkaline pH. NhaA is also believed to be responsible for adaptation to alkaline pH when sodium is available. NhaA is one of the three known sodium ion/proton antiporters in Escherichia coli along with NhaB and ChaA, though there are other mechanisms for Na+ extrusion such as NDH-I complicating the determination of the precise roles of each of the transporters [PUBMED:19448069].

Gene Ontology

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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 CPA_AT (CL0064), which has the following description:

This Clan contains transporter proteins that belong to the CPA superfamily and AT superfamily according to TCDB [1].

The clan contains the following 13 members:

Asp-Al_Ex Cons_hypoth698 DUF340 DUF4137 DUF819 DUF897 Glt_symporter KdgT Mem_trans Na_H_antiport_1 Na_H_Exchanger OAD_beta SBF

Alignments

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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.

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(17)
Full
(2392)
Representative proteomes NCBI
(1704)
Meta
(1782)
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(161)
RP35
(342)
RP55
(452)
RP75
(527)
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  Seed
(17)
Full
(2392)
Representative proteomes NCBI
(1704)
Meta
(1782)
RP15
(161)
RP35
(342)
RP55
(452)
RP75
(527)
Alignment:
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  Seed
(17)
Full
(2392)
Representative proteomes NCBI
(1704)
Meta
(1782)
RP15
(161)
RP35
(342)
RP55
(452)
RP75
(527)
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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.

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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.

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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_1828 (release 10.0)
Previous IDs: none
Type: Family
Author: Vella Briffa B
Number in seed: 17
Number in full: 2392
Average length of the domain: 354.40 aa
Average identity of full alignment: 44 %
Average coverage of the sequence by the domain: 91.60 %

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 19.8 19.8
Trusted cut-off 20.5 20.4
Noise cut-off 19.1 19.1
Model length: 378
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Na_H_antiport_1

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 Na_H_antiport_1 domain has been found. There are 3 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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