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306  structures 6378  species 0  interactions 36719  sequences 184  architectures

Family: Proton_antipo_M (PF00361)

Summary: Proton-conducting membrane transporter

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 "Membrane transport protein". More...

Membrane transport protein Edit Wikipedia article

A transport protein is a protein involved in facilitated diffusion. Changes in the conformation move the binding site to the opposite side of the protein.

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

This is the Wikipedia entry entitled "NADH dehydrogenase (ubiquinone)". More...

NADH dehydrogenase (ubiquinone) Edit Wikipedia article

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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.

Proton-conducting membrane transporter Provide feedback

This is a family of membrane transporters that inlcudes some 7 of potentially 14-16 TM regions. In many instances the family forms part of complex I that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N [1]. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction [2]. The family in total represents homologues across the phyla.

Literature references

  1. Walker JE; , Q Rev Biophys 1992;25:253-324.: The NADH:ubiquinone oxidoreductase (complex I) of respiratory chains. PUBMED:1470679 EPMC:1470679

  2. Morino M, Suzuki T, Ito M, Krulwich TA;, J Bacteriol. 2014;196:28-35.: Purification and functional reconstitution of a seven-subunit mrp-type na+/h+ antiporter. PUBMED:24142251 EPMC:24142251


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001750

Mrp-type antiporters comprise the cation/proton antiporter family 3 (CPA3), commonly referred to as Mrp. They are the products of operons that carry either six or seven genes (mrpA-G), and form complexes containing all subunits [ PUBMED:15980940 , PUBMED:18408029 ]. They have Na(+)/H(+) antiporter activity [ PUBMED:24142251 ]. Two of the Mrp proteins, MrpA and MrpD, resemble NuoL/ND5, NuoM/ND4, NuoN/ND2, the homologous subunits that constitute the membrane-embedded, proton-translocating core of complex I [ PUBMED:12914915 , PUBMED:20826797 , PUBMED:12460669 , PUBMED:20595580 ]. They also resemble subunits of membrane-bound hydrogenases, such as HyfB, HyfD and HyfF from E.coli [ PUBMED:9387241 ] and F420H2 dehydrogenasa (FPO complex) subunits L, N and M [ PUBMED:10751389 ].

This domain is found in subunits NuoL/ND5, NuoM/ND4, and NuoN/ND2 of the NADH:quinone oxidoreductase (complex I), Mrp antiporters subunits A and D, and in membrane subunits of hydrogenase complexes, such as hydrogenase-4 and F420H2 dehydrogenase.

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 ComplexI-N (CL0425), which has the following description:

This superfamily contains proteins from the families Oxidored_q1 and NADHdeh_related. The Oxidored_q1 family is part of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane. Many members of the NADHdeh_related family are archaeal and bacterial, indicating the evolutionary origins of ComplexI.

The clan contains the following 3 members:

NADHdeh_related NADHdh Proton_antipo_M

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
(14)
Full
(36719)
Representative proteomes UniProt
(422044)
RP15
(5206)
RP35
(18106)
RP55
(37908)
RP75
(64064)
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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
(14)
Full
(36719)
Representative proteomes UniProt
(422044)
RP15
(5206)
RP35
(18106)
RP55
(37908)
RP75
(64064)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(14)
Full
(36719)
Representative proteomes UniProt
(422044)
RP15
(5206)
RP35
(18106)
RP55
(37908)
RP75
(64064)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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.

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_4 (release 1.0)
Previous IDs: oxidored_q1; Oxidored_q1;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Eberhardt R
Number in seed: 14
Number in full: 36719
Average length of the domain: 280.3 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 51.06 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.5 21.5
Trusted cut-off 21.5 21.5
Noise cut-off 21.4 21.4
Model length: 293
Family (HMM) version: 23
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 Proton_antipo_M domain has been found. There are 306 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
A0A044RSJ4 View 3D Structure Click here
A0A044RSK1 View 3D Structure Click here
A0A077YYM7 View 3D Structure Click here
A0A077ZHZ2 View 3D Structure Click here
A0A077ZIG2 View 3D Structure Click here
A0A077ZK16 View 3D Structure Click here
A0A077ZK74 View 3D Structure Click here
A0A077ZLX7 View 3D Structure Click here
A0A077ZM38 View 3D Structure Click here
A0A077ZPX1 View 3D Structure Click here
A0A077ZQ97 View 3D Structure Click here
A0A077ZQL6 View 3D Structure Click here
A0A0H3GT15 View 3D Structure Click here
A0A0H3GVP8 View 3D Structure Click here
A0A0H3GWA2 View 3D Structure Click here
A0A0H3GX92 View 3D Structure Click here
A0A0K0EK50 View 3D Structure Click here
A0A0K0JHR1 View 3D Structure Click here
A0A0N4US56 View 3D Structure Click here
A0A0P0WBC4 View 3D Structure Click here
A0A0R0C7N6 View 3D Structure Click here
A0A0R0G2Z7 View 3D Structure Click here
A0A0R0GBL4 View 3D Structure Click here
A0A0R0HE12 View 3D Structure Click here
A0A0R0HRS5 View 3D Structure Click here
A0A0R0LAY8 View 3D Structure Click here
A0A1C1C619 View 3D Structure Click here
A0A1C1C626 View 3D Structure Click here
A0A1C1C648 View 3D Structure Click here
A0A1I7Q5G1 View 3D Structure Click here
A0A2P2CLC5 View 3D Structure Click here
A0A2P2CLE9 View 3D Structure Click here
A0A2P2CLG4 View 3D Structure Click here
A0A367GJ92 View 3D Structure Click here
A0A3P7DR98 View 3D Structure Click here
A0A3P7DZB9 View 3D Structure Click here
A0A3P7STQ7 View 3D Structure Click here
A0A3Q0KVE2 View 3D Structure Click here
A0A3Q0KVH1 View 3D Structure Click here
A0KJ55 View 3D Structure Click here