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199  structures 3998  species 7  interactions 10556  sequences 121  architectures

Family: Flavodoxin_1 (PF00258)

Summary: Flavodoxin

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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 Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008254

This domain is found in a number of proteins including flavodoxin and nitric-oxide synthase. Flavodoxins are electron-transfer proteins that function in various electron transport systems. They bind one FMN molecule, which serves as a redox-active prosthetic group [PUBMED:2597140] and are functionally interchangeable with ferredoxins. They have been isolated from prokaryotes, cyanobacteria, and some eukaryotic algae. Nitric oxide synthase (EC) produces nitric oxide from L-arginie and NADPH. Nitric oxide acts as a messenger molecule in the body.

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 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
(92)
Full
(10556)
Representative proteomes NCBI
(8477)
Meta
(791)
RP15
(813)
RP35
(1530)
RP55
(2194)
RP75
(2717)
Jalview View  View  View  View  View  View  View  View 
HTML View    View  View  View  View     
PP/heatmap 1   View  View  View  View     
Pfam viewer View  View             

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(92)
Full
(10556)
Representative proteomes NCBI
(8477)
Meta
(791)
RP15
(813)
RP35
(1530)
RP55
(2194)
RP75
(2717)
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
(92)
Full
(10556)
Representative proteomes NCBI
(8477)
Meta
(791)
RP15
(813)
RP35
(1530)
RP55
(2194)
RP75
(2717)
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: Prosite
Previous IDs: flavodoxin;
Type: Domain
Author: Finn RD
Number in seed: 92
Number in full: 10556
Average length of the domain: 138.50 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 32.80 %

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 24.4 23.2
Trusted cut-off 24.4 23.2
Noise cut-off 24.3 23.1
Model length: 143
Family (HMM) version: 20
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 7 interactions for this family. More...

Flavodoxin_1 NAD_binding_1 p450 Lactamase_B FMN_red Flavodoxin_2 FAD_binding_1

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_1 domain has been found. There are 199 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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