Summary: Flavodoxin domain
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Flavodoxin domain Provide feedback
This is a family of flavodoxins. Flavodoxins are electron transfer proteins that carry a molecule of non-covalently bound FMN.
Internal database links
SCOOP: | Flavodoxin_1 Flavodoxin_2 Flavodoxin_3 Flavodoxin_4 Flavodoxin_NdrI FMN_red |
Similarity to PfamA using HHSearch: | Flavodoxin_1 FMN_red Flavodoxin_3 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR026816
This entry represents the flavodoxin domain. Proteins with this domain include protoporphyrinogen IX dehydrogenase (HemG). HemG catalyses the 6-electron oxidation of protoporphyrinogen-IX to form protoporphyrin-IX using menaquinone as electron acceptor [ PUBMED:7788523 , PUBMED:7916647 ].
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...
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 (34) |
Full (3214) |
Representative proteomes | UniProt (15217) |
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RP15 (481) |
RP35 (1719) |
RP55 (3321) |
RP75 (5466) |
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Jalview | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (34) |
Full (3214) |
Representative proteomes | UniProt (15217) |
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---|---|---|---|---|---|---|---|
RP15 (481) |
RP35 (1719) |
RP55 (3321) |
RP75 (5466) |
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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:Q186N5_CLOD6 |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 34 |
Number in full: | 3214 |
Average length of the domain: | 129.8 aa |
Average identity of full alignment: | 17 % |
Average coverage of the sequence by the domain: | 65.39 % |
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: | 144 | ||||||||||||
Family (HMM) version: | 10 | ||||||||||||
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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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.