!!

Powering down the Pfam website
On October 5th, we began redirecting traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro). The Pfam website will remain available at pfam-legacy.xfam.org until January 2023, when it will be decommissioned. You can read more about the sunset period in our blog post.

Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
335  structures 4807  species 0  interactions 11940  sequences 38  architectures

Family: Flavodoxin_2 (PF02525)

Summary: Flavodoxin-like fold

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Flavodoxin-like fold Provide feedback

This family consists of a domain with a flavodoxin-like fold. The family includes bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) EC:1.6.99.2. These enzymes catalyse the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species [1]. This enzyme uses a FAD co-factor. The equation for this reaction is:- NAD(P)H + acceptor <=> NAD(P)(+) + reduced acceptor. This enzyme is also involved in the bioactivation of prodrugs used in chemotherapy [1]. The family also includes acyl carrier protein phosphodiesterase EC:3.1.4.14. This enzyme converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine residue from ACP [2]. This family is related to PF03358 and PF00258.

Literature references

  1. Li R, Bianchet MA, Talalay P, Amzel LM; , Proc Natl Acad Sci U S A 1995;92:8846-8850.: The three-dimensional structure of NAD(P)H:quinone reductase, a flavoprotein involved in cancer chemoprotection and chemotherapy: mechanism of the two-electron reduction PUBMED:7568029 EPMC:7568029

  2. Fischl AS, Kennedy EP; , J Bacteriol 1990;172:5445-5449.: Isolation and properties of acyl carrier protein phosphodiesterase of Escherichia coli. PUBMED:2168383 EPMC:2168383


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003680

This entry represents a domain with a flavodoxin-like fold.

Proteins with this domain include bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) EC . These enzymes catalyse the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species [ PUBMED:2168383 ]. This enzyme uses a FAD cofactor. The equation for this reaction is NAD(P)H + acceptor = NAD(P)(+) + reduced acceptor. This enzyme is also involved in the bioactivation of prodrugs used in chemotherapy [ PUBMED:2168383 ]. This domain is also found in acyl carrier protein phosphodiesterase EC . This enzyme converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine residue from ACP [ PUBMED:7568029 ].

Domain organisation

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

Loading domain graphics...

Pfam Clan

This family is a member of clan Flavoprotein (CL0042), which has the following description:

Members of this clan are FMN or FAD-binding redox proteins. Flavoproteins act in various electron-transport systems as functional analogues of ferredoxin. They are characterised by an open twisted alpha/beta structure consisting of five parallel beta-sheets connected by alpha-helices which surround the sheet.

The clan contains the following 7 members:

Flavodoxin_1 Flavodoxin_2 Flavodoxin_3 Flavodoxin_4 Flavodoxin_5 Flavodoxin_NdrI FMN_red

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
(240)
Full
(11940)
Representative proteomes UniProt
(65727)
RP15
(978)
RP35
(4773)
RP55
(11977)
RP75
(24093)
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
(240)
Full
(11940)
Representative proteomes UniProt
(65727)
RP15
(978)
RP35
(4773)
RP55
(11977)
RP75
(24093)
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
(240)
Full
(11940)
Representative proteomes UniProt
(65727)
RP15
(978)
RP35
(4773)
RP55
(11977)
RP75
(24093)
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_1456 (release 5.4)
Previous IDs: NADHdh_2;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bashton M , Bateman A
Number in seed: 240
Number in full: 11940
Average length of the domain: 187.2 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 89.61 %

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 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 198
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 Flavodoxin_2 domain has been found. There are 335 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.

Loading structure mapping...

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
A0A077ZKF9 View 3D Structure Click here
A0A077ZN29 View 3D Structure Click here
A0A0D2DN55 View 3D Structure Click here
A0A0H3GJ33 View 3D Structure Click here
A0A0H3GR45 View 3D Structure Click here
A0A0H3GSP2 View 3D Structure Click here
A0A0H3GU46 View 3D Structure Click here
A0A0H3GU63 View 3D Structure Click here
A0A0H3GXR4 View 3D Structure Click here
A0A0H3GY29 View 3D Structure Click here
A0A1C1D390 View 3D Structure Click here
A0A2R8PW65 View 3D Structure Click here
A1KAY0 View 3D Structure Click here
A1SB44 View 3D Structure Click here
A1SUA7 View 3D Structure Click here
A1VMH6 View 3D Structure Click here
A1W8C6 View 3D Structure Click here
A3QIU7 View 3D Structure Click here
A4G2N3 View 3D Structure Click here
A4Z112 View 3D Structure Click here
A5GAC6 View 3D Structure Click here
A6W4I5 View 3D Structure Click here
A7IDY1 View 3D Structure Click here
A8AGG0 View 3D Structure Click here
A8ALQ5 View 3D Structure Click here
A8AQP1 View 3D Structure Click here
A8FA13 View 3D Structure Click here
A8I0R2 View 3D Structure Click here
A8LAY7 View 3D Structure Click here
A9C3B1 View 3D Structure Click here
A9H9I9 View 3D Structure Click here
A9I4K2 View 3D Structure Click here
A9KM25 View 3D Structure Click here
A9MQG7 View 3D Structure Click here
A9MQU9 View 3D Structure Click here
B1M4X4 View 3D Structure Click here
B1XW54 View 3D Structure Click here
B1ZKG7 View 3D Structure Click here
B1ZNL9 View 3D Structure Click here
B2FKE2 View 3D Structure Click here