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93  structures 5613  species 0  interactions 8791  sequences 127  architectures

Family: Fer4_17 (PF13534)

Summary: 4Fe-4S dicluster domain

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4Fe-4S dicluster domain Provide feedback

This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.

Internal database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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 4Fe-4S (CL0344), which has the following description:

Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.

The clan contains the following 29 members:

ETF_QO Fer4 Fer4_10 Fer4_11 Fer4_12 Fer4_13 Fer4_14 Fer4_15 Fer4_16 Fer4_17 Fer4_18 Fer4_19 Fer4_2 Fer4_20 Fer4_21 Fer4_22 Fer4_23 Fer4_24 Fer4_3 Fer4_4 Fer4_5 Fer4_6 Fer4_7 Fer4_8 Fer4_9 FeS Molybdop_Fe4S4 Nitr_red_alph_N RLI

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
(69)
Full
(8791)
Representative proteomes UniProt
(37204)
RP15
(1421)
RP35
(4413)
RP55
(8282)
RP75
(13521)
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
(69)
Full
(8791)
Representative proteomes UniProt
(37204)
RP15
(1421)
RP35
(4413)
RP55
(8282)
RP75
(13521)
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
(69)
Full
(8791)
Representative proteomes UniProt
(37204)
RP15
(1421)
RP35
(4413)
RP55
(8282)
RP75
(13521)
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: Jackhmmer:B8J3I4
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 69
Number in full: 8791
Average length of the domain: 72.30 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 17.86 %

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 22.2 22.2
Trusted cut-off 22.2 22.2
Noise cut-off 22.1 22.1
Model length: 61
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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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Tree controls

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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 Fer4_17 domain has been found. There are 93 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
A0A0R0FV32 View 3D Structure Click here
A0A0R4J5X9 View 3D Structure Click here
A0A1D6EPD2 View 3D Structure Click here
A5PL98 View 3D Structure Click here
A8WPF0 View 3D Structure Click here
B0BM36 View 3D Structure Click here
O29748 View 3D Structure Click here
P07014 View 3D Structure Click here
P21801 View 3D Structure Click here
P21911 View 3D Structure Click here
P21912 View 3D Structure Click here
P21913 View 3D Structure Click here
P21914 View 3D Structure Click here
P32420 View 3D Structure Click here
P33393 View 3D Structure Click here
Q007T0 View 3D Structure Click here
Q09545 View 3D Structure Click here
Q1RGP3 View 3D Structure Click here
Q3T189 View 3D Structure Click here
Q4CP05 View 3D Structure Click here
Q4CVH2 View 3D Structure Click here
Q55CC2 View 3D Structure Click here
Q59QN7 View 3D Structure Click here
Q6FWS8 View 3D Structure Click here
Q6H4G3 View 3D Structure Click here
Q75CI4 View 3D Structure Click here
Q8I5S5 View 3D Structure Click here
Q8LB02 View 3D Structure Click here
Q8LBZ7 View 3D Structure Click here
Q8TSY4 View 3D Structure Click here
Q8ZQU2 View 3D Structure Click here
Q9CQA3 View 3D Structure Click here
Q9FJP9 View 3D Structure Click here
Q9S827 View 3D Structure Click here
Q9VWN3 View 3D Structure Click here
Q9YHT2 View 3D Structure Click here
Q9ZEA1 View 3D Structure Click here