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18  structures 56076  species 7  interactions 182124  sequences 80  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 membrane transport protein (or simply transporter) is a membrane protein[1] involved in the movement of ions, small molecules, or macromolecules, such as another protein, across a biological membrane. Transport proteins are integral transmembrane proteins; that is they exist permanently within and span the membrane across which they transport substances. The proteins may assist in the movement of substances by facilitated diffusion or active transport. These mechanisms of action are known as carrier-mediated transport.[2]

Difference between protein channels and protein carriers

  • Cavity in a carrier protein is not open simultaneously to the both environment (extracellular and intracellular). Either its inner gate is open, or outer gate is open, Carrier has binding sites, but porins and channel proteins have not. When a channel is opened, thousands to millions of ions can pass through the membrane in one time, but only one or a small amount of molecules can pass through a carrier molecule.


(Grouped by Transporter Classification database categories)

1: Channels/pores

Facilitated diffusion occurs in and out of the cell membrane via channels/pores and carriers/porters.


  • Channels:

Channels are either in open state or closed state. When a channel is opened with a slight conformational switch, it is open to both environment simultaneously (extracellular and intracellular)

  • Pores:

Pores are continuously open to these both environment, because they do not undergo conformational changes. They are always open.

2: Electrochemical potential-driven transporters

3: Primary active transporters

4: Group translocators

The group translocators provide a special mechanism for the phosphorylation of sugars as they are transported into bacteria (PEP group translocation)

5: Electron carriers

The transmembrane electron transfer carriers in the membrane include two-electron carriers, such as the disulfide bond oxidoreductases (DsbB and DsbD in E. coli) as well as one-electron carriers such as NADPH oxidase. Often these redox proteins are not considered transport proteins.

See also


External links

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". More...

NADH dehydrogenase Edit Wikipedia article

NADH dehydrogenase
EC number
CAS number 9079-67-8
IntEnz IntEnz view
ExPASy NiceZyme view
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum

NADH dehydrogenase (EC, cytochrome c reductase, type 1 dehydrogenase, beta-NADH dehydrogenase dinucleotide, diaphorase, dihydrocodehydrogenase I dehydrogenase, dihydronicotinamide adenine dinucleotide dehydrogenase, diphosphopyridine diaphorase, DPNH diaphorase, NADH diaphorase, NADH hydrogenase, NADH oxidoreductase, NADH-menadione oxidoreductase, reduced diphosphopyridine nucleotide diaphorase) is an enzyme with systematic name NADH:acceptor oxidoreductase.[1][2][3][4] This enzyme catalyses the following chemical reaction

NADH + H+ + acceptor \rightleftharpoons NAD+ + reduced acceptor

NADH dehydrogenase is a flavoprotein that contains iron-sulfur centres.


  1. ^ Adachi, K. and Okuyama, T. (1972). "Study on the reduced pyridine nucleotide dehydrogenase of bovine erythrocytes. I. Crystallization and properties of the reduced pyridine nucleotide dehydrogenase of bovine erythrocytes". Biochim. Biophys. Acta 268: 629–637. doi:10.1016/0005-2744(72)90266-5. PMID 4402556. 
  2. ^ Hatefi, Y., Ragan, C.I. and Galante, Y.M. (1985). "The enzymes and the enzyme complexes of the mitochondrial oxidative phosphorylation system". In Martonosi, A. The Enzymes of Biological Membranes 4 (2nd ed.). New York: Plenum Press. pp. 1–70. 
  3. ^ Hochstein, L.I. and Dalton, B.P. (1973). "Studies of a halophilic NADH dehydrogenase. I. Purification and properties of the enzyme". Biochim. Biophys. Acta 302: 216–228. doi:10.1016/0005-2744(73)90150-2. PMID 4144655. 
  4. ^ Kaniuga, Z. (1963). "The transformation of mitochondrial NADH dehydrogenase into NADH:Cytochrome c oxidoreductase". Biochim. Biophys. Acta 73: 550–564. doi:10.1016/0926-6569(63)90175-5. PMID 14074130. 

See also

External links

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

  • This is a redirect from a page that has been moved (renamed). This page was kept as a redirect to avoid breaking links, both internal and external, that may have been made to the old page name. For more information follow the bold category link.

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

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001750

NADH:ubiquinone oxidoreductase (complex I) (EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) [PUBMED:1470679]. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [PUBMED:10940377], mitochondria, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins [PUBMED:18394423].

This domain is found in several subunits of the NADH:ubiquinone oxidoreductase (complex I) and NADH-plastoquinone oxidoreductase [PUBMED:1470679].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 2 members:

NADHdeh_related Proton_antipo_M


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...

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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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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...


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
Author: Finn RD, Eberhardt R
Number in seed: 14
Number in full: 182124
Average length of the domain: 257.40 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 56.63 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -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: 16
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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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There are 7 interactions for this family. More...

Oxidored_q4 Proton_antipo_N Oxidored_q3 Oxidored_q2 Proton_antipo_M Oxidored_q3 Oxidored_q2


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 18 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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