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331  structures 5704  species 0  interactions 17895  sequences 325  architectures

Family: Flavodoxin_1 (PF00258)

Summary: Flavodoxin

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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-arginine and NADPH. Nitric oxide acts as a messenger molecule in the body.

The flavodoxin-like domain is an around 170-residue domain with a flavin mononucleotide (FMN)-binding site. It is involved in electron transfer reactions [ PUBMED:8160268 , PUBMED:7756978 ].

Structure analyses of several flavodoxin-like domains have shown that it is a wound alpha-beta-alpha fold with a central 5-stranded parallel hydrophobic beta-sheet flanked on either side by amphipathic alpha-helices [ PUBMED:9237990 , PUBMED:10048323 , PUBMED:10610791 ]. The FMN is positioned at the tip of the C-terminal side of the beta-sheet [ PUBMED:9237990 ]. The fold correlates with a highly conserved, repetitive sequence pattern in which hydrophobic residues cluster in beta-strands and have a 3-4-residue periodicity in alpha-helices [ PUBMED:7756978 ].

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 (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
(59)
Full
(17895)
Representative proteomes UniProt
(68933)
RP15
(2681)
RP35
(8050)
RP55
(15832)
RP75
(26218)
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
(59)
Full
(17895)
Representative proteomes UniProt
(68933)
RP15
(2681)
RP35
(8050)
RP55
(15832)
RP75
(26218)
Alignment:
Format:
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Sequence:
Gaps:
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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
(59)
Full
(17895)
Representative proteomes UniProt
(68933)
RP15
(2681)
RP35
(8050)
RP55
(15832)
RP75
(26218)
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: Prosite
Previous IDs: flavodoxin;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 59
Number in full: 17895
Average length of the domain: 138.20 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 21.82 %

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 25.0 25.0
Trusted cut-off 25.0 25.0
Noise cut-off 24.9 24.9
Model length: 143
Family (HMM) version: 27
Download: download the raw HMM for this family

Species distribution

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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 Flavodoxin_1 domain has been found. There are 331 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
A0A0R0FIC1 View 3D Structure Click here
A0A0R0GAG6 View 3D Structure Click here
A0A0R0L4H1 View 3D Structure Click here
A0A0R4IQG7 View 3D Structure Click here
A0A0R4J338 View 3D Structure Click here
A0A0R4J4Q1 View 3D Structure Click here
A0A0R4J5H8 View 3D Structure Click here
A0A1D6DVQ5 View 3D Structure Click here
A0A1D6IAL1 View 3D Structure Click here
A0A1D6L6E5 View 3D Structure Click here
A0A1D6ND25 View 3D Structure Click here
A0A1D6QVJ3 View 3D Structure Click here
A0A1D8PHL8 View 3D Structure Click here
A0A1D8PLR7 View 3D Structure Click here
A0A1D8PPU8 View 3D Structure Click here
A0A2R8QQ95 View 3D Structure Click here
A2AI05 View 3D Structure Click here
A2BIN8 View 3D Structure Click here
A4HSJ7 View 3D Structure Click here
A4I3K3 View 3D Structure Click here
A4IA43 View 3D Structure Click here
A4IBG5 View 3D Structure Click here
A4IDQ0 View 3D Structure Click here
B5DF48 View 3D Structure Click here
C0H553 View 3D Structure Click here
C0HFL6 View 3D Structure Click here
D4ABT4 View 3D Structure Click here
F1Q7F3 View 3D Structure Click here
F1QML0 View 3D Structure Click here
F8W4Z6 View 3D Structure Click here
I1K9R6 View 3D Structure Click here
I1MB07 View 3D Structure Click here
I1N5D0 View 3D Structure Click here
K7THB1 View 3D Structure Click here
K7TVP4 View 3D Structure Click here
M1ZMI3 View 3D Structure Click here
O23207 View 3D Structure Click here
O59761 View 3D Structure Click here
O94613 View 3D Structure Click here
P00388 View 3D Structure Click here
P03817 View 3D Structure Click here
P0ABY4 View 3D Structure Click here
P16435 View 3D Structure Click here
P16603 View 3D Structure Click here
P29474 View 3D Structure Click here
P29475 View 3D Structure Click here
P29476 View 3D Structure Click here
P29477 View 3D Structure Click here
P35228 View 3D Structure Click here
P36587 View 3D Structure Click here
P37040 View 3D Structure Click here
P38038 View 3D Structure Click here
P47169 View 3D Structure Click here
P61949 View 3D Structure Click here
P65367 View 3D Structure Click here
P70313 View 3D Structure Click here
Q06518 View 3D Structure Click here
Q08960 View 3D Structure Click here
Q08C92 View 3D Structure Click here
Q09590 View 3D Structure Click here
Q0J705 View 3D Structure Click here
Q12181 View 3D Structure Click here
Q17574 View 3D Structure Click here
Q1K9C2 View 3D Structure Click here
Q27571 View 3D Structure Click here
Q27597 View 3D Structure Click here
Q2FUZ8 View 3D Structure Click here
Q46877 View 3D Structure Click here
Q498R1 View 3D Structure Click here
Q4CKR7 View 3D Structure Click here
Q4CQR2 View 3D Structure Click here
Q4CXG8 View 3D Structure Click here
Q4D617 View 3D Structure Click here
Q4DLF5 View 3D Structure Click here
Q4DPU7 View 3D Structure Click here
Q4DS22 View 3D Structure Click here
Q54B10 View 3D Structure Click here
Q54JL0 View 3D Structure Click here
Q55CT1 View 3D Structure Click here
Q57954 View 3D Structure Click here
Q58142 View 3D Structure Click here
Q58158 View 3D Structure Click here
Q5AD27 View 3D Structure Click here
Q5JL61 View 3D Structure Click here
Q62600 View 3D Structure Click here
Q653S9 View 3D Structure Click here
Q6NPS8 View 3D Structure Click here
Q6NUM6 View 3D Structure Click here
Q6PFP6 View 3D Structure Click here
Q7X7K8 View 3D Structure Click here
Q8BJM7 View 3D Structure Click here
Q8C1A3 View 3D Structure Click here
Q8H8N3 View 3D Structure Click here
Q8I3L6 View 3D Structure Click here
Q8IKX3 View 3D Structure Click here
Q8RXN5 View 3D Structure Click here
Q9N535 View 3D Structure Click here
Q9NV66 View 3D Structure Click here
Q9SB48 View 3D Structure Click here
Q9SUM3 View 3D Structure Click here
Q9UBK8 View 3D Structure Click here
Q9UHB4 View 3D Structure Click here
Q9VSJ5 View 3D Structure Click here
Q9Z0J4 View 3D Structure Click here