Summary: Flavodoxin domain
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Flavodoxin domain Provide feedback
This family represents a flavodoxin domain.
Internal database links
SCOOP: | AAA_22 AAA_30 Flavodoxin_1 Flavodoxin_2 Flavodoxin_4 Flavodoxin_5 Flavodoxin_NdrI FMN_red FtsK_SpoIIIE SRP54 |
Similarity to PfamA using HHSearch: | Flavodoxin_1 Flavodoxin_5 |
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.
Molecular function | FMN binding (GO:0010181) |
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_redAlignments
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...
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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 (16) |
Full (524) |
Representative proteomes | UniProt (2555) |
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RP15 (92) |
RP35 (311) |
RP55 (547) |
RP75 (893) |
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Jalview | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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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 (16) |
Full (524) |
Representative proteomes | UniProt (2555) |
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RP15 (92) |
RP35 (311) |
RP55 (547) |
RP75 (893) |
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Raw Stockholm | |||||||
Gzipped |
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
Seed source: | Jackhmmer:Q180M7 |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 16 |
Number in full: | 524 |
Average length of the domain: | 147.2 aa |
Average identity of full alignment: | 25 % |
Average coverage of the sequence by the domain: | 85.93 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 160 | ||||||||||||
Family (HMM) version: | 10 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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