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188  structures 2899  species 3  interactions 7847  sequences 15  architectures

Family: Flavodoxin_2 (PF02525)

Summary: Flavodoxin-like fold

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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


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...

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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(247)
Full
(7847)
Representative proteomes NCBI
(11821)
Meta
(2314)
RP15
(410)
RP35
(843)
RP55
(1194)
RP75
(1533)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(247)
Full
(7847)
Representative proteomes NCBI
(11821)
Meta
(2314)
RP15
(410)
RP35
(843)
RP55
(1194)
RP75
(1533)
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
(247)
Full
(7847)
Representative proteomes NCBI
(11821)
Meta
(2314)
RP15
(410)
RP35
(843)
RP55
(1194)
RP75
(1533)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

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.

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
Author: Bashton M, Bateman A
Number in seed: 247
Number in full: 7847
Average length of the domain: 183.60 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 92.92 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.5 20.5
Trusted cut-off 20.5 20.5
Noise cut-off 20.4 20.4
Model length: 199
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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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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Interactions

There are 3 interactions for this family. More...

Flavodoxin_1 Flavodoxin_2 FMN_red

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 188 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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