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7  structures 3800  species 0  interactions 6092  sequences 79  architectures

Family: NFACT-R_1 (PF05670)

Summary: NFACT protein RNA binding domain

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

This is the Wikipedia entry entitled "Domain of unknown function". More...

Domain of unknown function Edit Wikipedia article

A Domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF188 and DUF1000. There are now over 3,000 DUF families within the Pfam database representing over 20% of known families.

History

The DUF naming scheme was introduced by Chris Ponting, through the addition of DUF1 and DUF2 to the SMART database.[1] These two domains were found to be widely distributed in bacterial signaling proteins. Subsequently, the functions of these domains were identified and they have since been renamed as the GGDEF domain and EAL domain respectively.

Structure

Structural genomics programmes have attempted to understand the function of DUFs through structure determination. The structures of over 250 DUF families have been solved.[2]

External Links

List of Pfam familes beginning with the letter D, including DUF families

References

  1. ^ Schultz J, Milpetz F, Bork P, Ponting CP (1998). "SMART, a simple modular architecture research tool: identification of signaling domains". Proc. Natl. Acad. Sci. U.S.A. 95 (11): 5857–64. PMC 34487. PMID 9600884. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ^ Jaroszewski L, Li Z, Krishna SS; et al. (2009). "Exploration of uncharted regions of the protein universe". PLoS Biol. 7 (9): e1000205. doi:10.1371/journal.pbio.1000205. PMC 2744874. PMID 19787035. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

NFACT protein RNA binding domain Provide feedback

This domain occurs in proteins that have been annotated as Fibronectin/fibrinogen binding protein by similarity. This annotation comes from O34693 where the N-terminal region is involved in this activity [1]. It is an RNA binding domain of the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins. This NFACT-R family is found in two eukaryotic gene contexts: fused to the NFACT-N and NFACT-C domains in the NFACT protein involved in the ribosomal quality control pathway which contributes to CAT-tailing and as a standalone domain [2]. Additionally this domain contains a conserved motif D/E-X-W/Y-X-H that may be functionally important.

Literature references

  1. Courtney HS, Li Y, Dale JB, Hasty DL; , Infect Immun 1994;62:3937-3946.: Cloning, sequencing, and expression of a fibronectin/fibrinogen-binding protein from group A streptococci. PUBMED:8063411 EPMC:8063411

  2. Burroughs AM, Aravind L;, RNA Biol. 2014;11:360-372.: A highly conserved family of domains related to the DNA-glycosylase fold helps predict multiple novel pathways for RNA modifications. PUBMED:24646681 EPMC:24646681


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008532

This domain occurs in proteins that have been annotated as fibronectin/fibrinogen binding protein by similarity. This annotation comes from SWISSPROT where the N-terminal region is involved in this activity [ PUBMED:8063411 ]. This entry represents an RNA binding domain in the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins. This domain is found in two eukaryotic gene contexts: fused to the NFACT-N and NFACT-C domains in the NFACT protein involved in the ribosomal quality control pathway which contributes to CAT-tailing, and as a standalone domain [ PUBMED:24646681 ]. Additionally this domain contains a conserved motif D/E-X-W/Y-X-H that may be functionally important.

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 NFACT_RNA-bind (CL0684), which has the following description:

This clan includes the RNA-binding domains found in the mammalian NEMF, drosophila caliban, yeast Tae2, and bacterial FpbA-like proteins (NFACT). The RNA-binding domain associated with this family is also observed in distinct architectural contexts in other proteins across phylogenetically diverse prokaryotes.It is found in two eukaryotic gene contexts: fused to the NFACT-N and NFACT-C domains in the NFACT protein involved in the ribosomal quality control pathway which contributes to CAT-tailing and as a standalone domain. In bacteria, it is mostly found fused to the ThiI domain as a variant of the canonical tRNA 4-thiouridylation pathway [1].

The clan contains the following 2 members:

NFACT-R_1 NFACT-R_2

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
(36)
Full
(6092)
Representative proteomes UniProt
(18790)
RP15
(1237)
RP35
(3129)
RP55
(5288)
RP75
(7765)
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
(36)
Full
(6092)
Representative proteomes UniProt
(18790)
RP15
(1237)
RP35
(3129)
RP55
(5288)
RP75
(7765)
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
(36)
Full
(6092)
Representative proteomes UniProt
(18790)
RP15
(1237)
RP35
(3129)
RP55
(5288)
RP75
(7765)
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_738 (Release 8.0)
Previous IDs: DUF814;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Iyer LM , Aravind L , Burroughs AM , El-Gebali S
Number in seed: 36
Number in full: 6092
Average length of the domain: 105.8 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 18.06 %

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 29.8 29.8
Trusted cut-off 29.8 29.8
Noise cut-off 29.7 29.7
Model length: 111
Family (HMM) version: 16
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 NFACT-R_1 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
A0A044SC60 View 3D Structure Click here
A0A044SLL4 View 3D Structure Click here
A0A044UR62 View 3D Structure Click here
A0A077YWW5 View 3D Structure Click here
A0A077Z628 View 3D Structure Click here
A0A0A2V2J5 View 3D Structure Click here
A0A0D2D951 View 3D Structure Click here
A0A0D2GZC9 View 3D Structure Click here
A0A0G2K9F2 View 3D Structure Click here
A0A0K0EMY2 View 3D Structure Click here
A0A0K0ERD8 View 3D Structure Click here
A0A0N4UHE3 View 3D Structure Click here
A0A0N4UIM5 View 3D Structure Click here
A0A0N4UJC1 View 3D Structure Click here
A0A144A0J9 View 3D Structure Click here
A0A175VPA2 View 3D Structure Click here
A0A175WBD7 View 3D Structure Click here
A0A1C1CJ96 View 3D Structure Click here
A0A1C1D0C0 View 3D Structure Click here
A0A1D6MX03 View 3D Structure Click here
A0A1D6NCH3 View 3D Structure Click here
A0A1D8PQD9 View 3D Structure Click here
A0A1D8PS32 View 3D Structure Click here
A0A3P7E5X3 View 3D Structure Click here
A0A3P7EEZ4 View 3D Structure Click here
A0A3Q0KDR2 View 3D Structure Click here
A0A3Q0KFX0 View 3D Structure Click here
A0A7I4KP65 View 3D Structure Click here
A4HU15 View 3D Structure Click here
A4I5N6 View 3D Structure Click here
A4VWG9 View 3D Structure Click here
B4G0U8 View 3D Structure Click here
C0NCP0 View 3D Structure Click here
C0NQN7 View 3D Structure Click here
C1GP69 View 3D Structure Click here
C6TB30 View 3D Structure Click here
D4AAU6 View 3D Structure Click here
I1K994 View 3D Structure Click here
I1L0M7 View 3D Structure Click here
I1MGB1 View 3D Structure Click here