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17  structures 1375  species 0  interactions 1736  sequences 5  architectures

Family: Flavodoxin_NdrI (PF07972)

Summary: NrdI Flavodoxin like

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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.

NrdI Flavodoxin like Provide feedback

No Pfam abstract.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004465

Ribonucleotide reductases (RNRs) are enzymes that provide the precursors of DNA synthesis. The three characterised classes of RNRs differ by their metal cofactor and their stable organic radical. Class Ib RNR is encoded in four different genes: nrdH, nrdI, nrdE and nrdF [ PUBMED:12686643 ]. The exact function of NrdI within the ribonucleotide reductases has not yet been fully characterised.

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
(53)
Full
(1736)
Representative proteomes UniProt
(9210)
RP15
(183)
RP35
(778)
RP55
(1797)
RP75
(3406)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(53)
Full
(1736)
Representative proteomes UniProt
(9210)
RP15
(183)
RP35
(778)
RP55
(1797)
RP75
(3406)
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
(53)
Full
(1736)
Representative proteomes UniProt
(9210)
RP15
(183)
RP35
(778)
RP55
(1797)
RP75
(3406)
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: Pfam-B_1603 (release 16.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 53
Number in full: 1736
Average length of the domain: 119.9 aa
Average identity of full alignment: 42 %
Average coverage of the sequence by the domain: 82.09 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 120
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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_NdrI domain has been found. There are 17 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
A0A0H3GX40 View 3D Structure Click here
A1BA96 View 3D Structure Click here
A1T6Q8 View 3D Structure Click here
A1UE06 View 3D Structure Click here
A1URS1 View 3D Structure Click here
A6TCU0 View 3D Structure Click here
A6X357 View 3D Structure Click here
A8ANN2 View 3D Structure Click here
A9MG06 View 3D Structure Click here
B2VDV1 View 3D Structure Click here
B8DVW3 View 3D Structure Click here
B9EAC8 View 3D Structure Click here
C5BUY7 View 3D Structure Click here
K0F4C2 View 3D Structure Click here
P0A772 View 3D Structure Click here
P0A774 View 3D Structure Click here
P0A775 View 3D Structure Click here
P47472 View 3D Structure Click here
P50618 View 3D Structure Click here
P68524 View 3D Structure Click here
P75460 View 3D Structure Click here
P9WIZ3 View 3D Structure Click here
Q0S2M1 View 3D Structure Click here
Q1GJB3 View 3D Structure Click here
Q1R0L8 View 3D Structure Click here
Q2G079 View 3D Structure Click here
Q2K3W4 View 3D Structure Click here
Q2YJZ2 View 3D Structure Click here
Q32CQ1 View 3D Structure Click here
Q49VS8 View 3D Structure Click here
Q4L4F3 View 3D Structure Click here
Q56109 View 3D Structure Click here
Q5HR00 View 3D Structure Click here
Q65JA6 View 3D Structure Click here
Q6D1W1 View 3D Structure Click here
Q6F0T6 View 3D Structure Click here
Q6MSC4 View 3D Structure Click here
Q73VB3 View 3D Structure Click here
Q7N772 View 3D Structure Click here
Q8D1U5 View 3D Structure Click here