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280  structures 6741  species 0  interactions 28788  sequences 221  architectures

Family: Oxidored_FMN (PF00724)

Summary: NADH:flavin oxidoreductase / NADH oxidase family

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NADH:flavin oxidoreductase / NADH oxidase family Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001155

The TIM-barrel fold is a closed barrel structure composed of an eight-fold repeat of beta-alpha units, where the eight parallel beta strands on the inside are covered by the eight alpha helices on the outside [ PUBMED:11257493 ]. It is a widely distributed fold which has been found in many enzyme families that catalyse completely unrelated reactions [ PUBMED:12206759 ]. The active site is always found at the C-terminal end of this domain.

Proteins in this entry are a variety of NADH:flavin oxidoreductase/NADH oxidase enzymes, found mostly in bacteria or fungi, that contain a TIM-barrel fold. They commonly use FMN/FAD as cofactor and include:

  • dimethylamine dehydrogenase
  • trimethylamine dehydrogenase
  • 12-oxophytodienoate reductase
  • NADPH dehydrogenase
  • NADH oxidase

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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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
(7)
Full
(28788)
Representative proteomes UniProt
(115022)
RP15
(3052)
RP35
(12365)
RP55
(26641)
RP75
(47438)
Jalview View  View  View  View  View  View  View 
HTML View             
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
(7)
Full
(28788)
Representative proteomes UniProt
(115022)
RP15
(3052)
RP35
(12365)
RP55
(26641)
RP75
(47438)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(7)
Full
(28788)
Representative proteomes UniProt
(115022)
RP15
(3052)
RP35
(12365)
RP55
(26641)
RP75
(47438)
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_642 (release 2.1)
Previous IDs: oxidored_FMN;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 7
Number in full: 28788
Average length of the domain: 312.00 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 72.37 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.3 20.3
Trusted cut-off 20.3 20.3
Noise cut-off 20.2 20.2
Model length: 342
Family (HMM) version: 22
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_FMN domain has been found. There are 280 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
A0A0R0FRL1 View 3D Structure Click here
A0A0R0GV25 View 3D Structure Click here
A0A1D8PMP0 View 3D Structure Click here
A0A1D8PPK1 View 3D Structure Click here
A0A1D8PPM0 View 3D Structure Click here
A0A1D8PPM9 View 3D Structure Click here
A0A1D8PRP2 View 3D Structure Click here
A4HSY5 View 3D Structure Click here
A4I8U6 View 3D Structure Click here
B0G116 View 3D Structure Click here
B4F872 View 3D Structure Click here
B4FLS8 View 3D Structure Click here
B9FFD2 View 3D Structure Click here
B9FFD3 View 3D Structure Click here
B9FSC8 View 3D Structure Click here
C6TDQ8 View 3D Structure Click here
E9AGH7 View 3D Structure Click here
E9AGH8 View 3D Structure Click here
E9AGH8 View 3D Structure Click here
I1JAQ7 View 3D Structure Click here
I1LFV5 View 3D Structure Click here
I1LY51 View 3D Structure Click here
I1MBY3 View 3D Structure Click here
I1MII7 View 3D Structure Click here
I1MSB2 View 3D Structure Click here
I1MSB3 View 3D Structure Click here
K7KKY3 View 3D Structure Click here
K7KSI5 View 3D Structure Click here
K7KSI8 View 3D Structure Click here
K7MWT5 View 3D Structure Click here
K7V5I3 View 3D Structure Click here
O16214 View 3D Structure Click here
O16215 View 3D Structure Click here
O50388 View 3D Structure Click here
O50431 View 3D Structure Click here
O76410 View 3D Structure Click here
O94467 View 3D Structure Click here
P0DI08 View 3D Structure Click here
P0DI09 View 3D Structure Click here
P41816 View 3D Structure Click here
P42593 View 3D Structure Click here
P77258 View 3D Structure Click here
Q03558 View 3D Structure Click here
Q09670 View 3D Structure Click here
Q09671 View 3D Structure Click here
Q0E0C6 View 3D Structure Click here
Q0JMR0 View 3D Structure Click here
Q20883 View 3D Structure Click here
Q23090 View 3D Structure Click here
Q23091 View 3D Structure Click here
Q2FZU7 View 3D Structure Click here
Q2G153 View 3D Structure Click here
Q49HD7 View 3D Structure Click here
Q49HD8 View 3D Structure Click here
Q49HD9 View 3D Structure Click here
Q49HE1 View 3D Structure Click here
Q49HE2 View 3D Structure Click here
Q4CNI1 View 3D Structure Click here
Q4DKB3 View 3D Structure Click here
Q4DTA6 View 3D Structure Click here
Q4DZ00 View 3D Structure Click here
Q4E4V7 View 3D Structure Click here
Q54C83 View 3D Structure Click here
Q54JW3 View 3D Structure Click here
Q54JW3 View 3D Structure Click here
Q54K64 View 3D Structure Click here
Q54L37 View 3D Structure Click here
Q54WS0 View 3D Structure Click here
Q55AQ8 View 3D Structure Click here
Q59W51 View 3D Structure Click here
Q5A0J5 View 3D Structure Click here
Q5A4J9 View 3D Structure Click here
Q5A894 View 3D Structure Click here
Q5ZC83 View 3D Structure Click here
Q5ZC83 View 3D Structure Click here
Q69TH4 View 3D Structure Click here
Q69TH6 View 3D Structure Click here
Q69TH8 View 3D Structure Click here
Q69TI0 View 3D Structure Click here
Q69TI2 View 3D Structure Click here
Q6Z965 View 3D Structure Click here
Q84QK0 View 3D Structure Click here
Q8GYA3 View 3D Structure Click here
Q8GYB8 View 3D Structure Click here
Q8LAH7 View 3D Structure Click here
Q9FUP0 View 3D Structure Click here
Q9N5C0 View 3D Structure Click here
Q9TXX0 View 3D Structure Click here