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106  structures 5930  species 0  interactions 11703  sequences 36  architectures

Family: Oxidored_q2 (PF00420)

Summary: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L

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 "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.

NADH-ubiquinone/plastoquinone oxidoreductase chain 4L Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR039428

This entry includes NADH:ubiquinone oxidoreductase, chain 4L and bacterial Mnh complex subunit C. They share significant protein sequence similarity [ PUBMED:17293423 ].

ADH: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 ]. In eukaryotes, NADH:ubiquinone oxidoreductase, chain 4L is usually found in either mitochondria or chloroplasts as part of the respiratory-chain NADH dehydrogenase (also known as complex I or NADH-ubiquinone oxidoreductase), an oligomeric enzymatic complex [ PUBMED:15843018 ]. However, it is also found in bacteria [ PUBMED:18307315 ] and archaea [ PUBMED:10940377 ] where it is annotated as NuoK subunit.

Mnh subunit C1 is a cation antiporter, involved in K(+) and Na(+) excretion [ PUBMED:17293423 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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
(61)
Full
(11703)
Representative proteomes UniProt
(80261)
RP15
(1549)
RP35
(5630)
RP55
(12173)
RP75
(20903)
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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
(61)
Full
(11703)
Representative proteomes UniProt
(80261)
RP15
(1549)
RP35
(5630)
RP55
(12173)
RP75
(20903)
Alignment:
Format:
Order:
Sequence:
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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
(61)
Full
(11703)
Representative proteomes UniProt
(80261)
RP15
(1549)
RP35
(5630)
RP55
(12173)
RP75
(20903)
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.

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_193 (release 1.0)
Previous IDs: oxidored_q2;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD
Number in seed: 61
Number in full: 11703
Average length of the domain: 98.7 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 85.26 %

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 26.1 26.1
Trusted cut-off 26.2 26.1
Noise cut-off 26.0 26.0
Model length: 105
Family (HMM) version: 27
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 Oxidored_q2 domain has been found. There are 106 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
A0A0G2JWA4 View 3D Structure Click here
A0A0H3H106 View 3D Structure Click here
A0A0R0FEW8 View 3D Structure Click here
A0A0R0IXM3 View 3D Structure Click here
A0A1C1C652 View 3D Structure Click here
A0A2P2CLH7 View 3D Structure Click here
A0A3B6U9Q8 View 3D Structure Click here
A0KJ58 View 3D Structure Click here
A0LDR7 View 3D Structure Click here
A0LEQ5 View 3D Structure Click here
A0LJM1 View 3D Structure Click here
A0LRJ1 View 3D Structure Click here
A0QU26 View 3D Structure Click here
A1AVS2 View 3D Structure Click here
A1B482 View 3D Structure Click here
A1E9X6 View 3D Structure Click here
A1K5B8 View 3D Structure Click here
A1SE37 View 3D Structure Click here
A1T696 View 3D Structure Click here
A1TLM6 View 3D Structure Click here
A1UD94 View 3D Structure Click here
A1USX7 View 3D Structure Click here
A2SFN6 View 3D Structure Click here
A4FPT1 View 3D Structure Click here
A4GYW8 View 3D Structure Click here
A4XC28 View 3D Structure Click here
A4XV11 View 3D Structure Click here
A4YVK0 View 3D Structure Click here
A5FXJ1 View 3D Structure Click here
A5G9A9 View 3D Structure Click here
A5GD03 View 3D Structure Click here
A5UVF9 View 3D Structure Click here
A6H1Q3 View 3D Structure Click here
A6Q1Q4 View 3D Structure Click here
A6QCF2 View 3D Structure Click here
A6TBW5 View 3D Structure Click here
A6X1M3 View 3D Structure Click here
A7GW60 View 3D Structure Click here
A7HIH8 View 3D Structure Click here
A7HY39 View 3D Structure Click here