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7  structures 5738  species 0  interactions 9443  sequences 88  architectures

Family: NifU (PF01106)

Summary: NifU-like domain

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NifU-like domain Provide feedback

This is an alignment of the carboxy-terminal domain. This is the only common region between the NifU protein from nitrogen-fixing bacteria and rhodobacterial species. The biochemical function of NifU is unknown [1].

Literature references

  1. Ouzounis C, Bork P, Sander C; , Trends Biochem Sci 1994;19:199-200.: The modular structure of NifU proteins. PUBMED:8048161 EPMC:8048161

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001075

Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] [ PUBMED:16221578 ]. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.

The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [ PUBMED:16211402 , PUBMED:16843540 ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly [ PUBMED:15937904 ].

The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA [ PUBMED:17350000 ]. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. SufA is homologous to IscA [ PUBMED:15278785 ], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets.

In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins [ PUBMED:11498000 ]. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen [ PUBMED:8875867 ].

This entry represents the C-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal ( INTERPRO ) and a C-terminal domain [ PUBMED:8048161 ]. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation.

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 NifU (CL0232), which has the following description:

This clan includes the C-terminal domain of NifU as well as a large family of uncharacterised domains.

The clan contains the following 2 members:

FeS_assembly_P NifU


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.

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

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Representative proteomes UniProt

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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.

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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...


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_1206 (release 3.0)
Previous IDs: NifU; NifU-like;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Bateman A
Number in seed: 432
Number in full: 9443
Average length of the domain: 66.7 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 34.5 %

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 26.8 26.9
Model length: 67
Family (HMM) version: 20
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


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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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The tree shows the occurrence of this domain across different species. More...


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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 NifU domain has been found. There are 7 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
B4H303 View 3D Structure Click here
B4IMF6 View 3D Structure Click here
B4JWR9 View 3D Structure Click here
B4M375 View 3D Structure Click here
B4NE93 View 3D Structure Click here
B4R3T1 View 3D Structure Click here
B5DKJ8 View 3D Structure Click here
B8A6A3 View 3D Structure Click here
C0H578 View 3D Structure Click here
C0NCG7 View 3D Structure Click here
C0P617 View 3D Structure Click here
C1GR31 View 3D Structure Click here
C3K9S0 View 3D Structure Click here
C4JAF3 View 3D Structure Click here
C4K405 View 3D Structure Click here
C4LA10 View 3D Structure Click here
C5BGT5 View 3D Structure Click here
C5BJC0 View 3D Structure Click here
C6TBQ1 View 3D Structure Click here
D3ZA85 View 3D Structure Click here
D4H031 View 3D Structure Click here
I1L1A7 View 3D Structure Click here
I1NBE8 View 3D Structure Click here
I1NJ75 View 3D Structure Click here
O25009 View 3D Structure Click here
O26025 View 3D Structure Click here
O32119 View 3D Structure Click here
P20628 View 3D Structure Click here
P31774 View 3D Structure Click here
P32860 View 3D Structure Click here
P57609 View 3D Structure Click here
P63020 View 3D Structure Click here
P63022 View 3D Structure Click here
P63023 View 3D Structure Click here
Q056Z1 View 3D Structure Click here
Q089F8 View 3D Structure Click here
Q0IU70 View 3D Structure Click here
Q0P7Y9 View 3D Structure Click here
Q0PBR5 View 3D Structure Click here
Q10MC1 View 3D Structure Click here