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49  structures 1341  species 0  interactions 2061  sequences 44  architectures

Family: NUDIX_2 (PF13869)

Summary: Nucleotide hydrolase

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.

Nucleotide hydrolase Provide feedback

Nudix hydrolases are found in all classes of organism and hydrolyse a wide range of organic pyrophosphates, including nucleoside di- and triphosphates, di-nucleoside and diphospho-inositol polyphosphates, nucleotide sugars and RNA caps, with varying degrees of substrate specificity.

Literature references

  1. Ruegsegger U, Beyer K, Keller W;, J Biol Chem. 1996;271:6107-6113.: Purification and characterization of human cleavage factor Im involved in the 3' end processing of messenger RNA precursors. PUBMED:8626397 EPMC:8626397

  2. McLennan AG;, Cell Mol Life Sci. 2006;63:123-143.: The Nudix hydrolase superfamily. PUBMED:16378245 EPMC:16378245


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR016706

This entry represents cleavage and polyadenylation specificity factor subunit 5, also known as the cleavage and polyadenylation specificity factor 25kDa subunit. These proteins are a component of the cleavage factor Im (CFIm) complex involved in pre-mRNA 3' end processing [ PUBMED:9659921 ]. CFIm may also play a role in regulation of poly(A) site selection [ PUBMED:20695905 ].

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 NUDIX (CL0261), which has the following description:

This superfamily contains the NUDIX family and one related family.

The clan contains the following 10 members:

DUF4743 DUF4916 Hexose_dehydrat MRP-L46 NUDIX NUDIX-like NUDIX_2 NUDIX_4 NUDIX_5 Nudix_hydro

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
(17)
Full
(2061)
Representative proteomes UniProt
(3303)
RP15
(406)
RP35
(999)
RP55
(1646)
RP75
(2142)
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
(17)
Full
(2061)
Representative proteomes UniProt
(3303)
RP15
(406)
RP35
(999)
RP55
(1646)
RP75
(2142)
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
(17)
Full
(2061)
Representative proteomes UniProt
(3303)
RP15
(406)
RP35
(999)
RP55
(1646)
RP75
(2142)
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:O43809
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 17
Number in full: 2061
Average length of the domain: 172.6 aa
Average identity of full alignment: 53 %
Average coverage of the sequence by the domain: 72.28 %

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 27.8 27.2
Noise cut-off 26.4 26.1
Model length: 188
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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The tree shows the occurrence of this domain across different species. More...

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 NUDIX_2 domain has been found. There are 49 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
A0A044RZ30 View 3D Structure Click here
A0A044TPR4 View 3D Structure Click here
A0A077YWI5 View 3D Structure Click here
A0A0D2GTN1 View 3D Structure Click here
A0A0J9Y1S1 View 3D Structure Click here
A0A0K0DW31 View 3D Structure Click here
A0A0N4UCU8 View 3D Structure Click here
A0A0R0G2B9 View 3D Structure Click here
A0A0R0IAV3 View 3D Structure Click here
A0A1C1C7E6 View 3D Structure Click here
A0A1D6JIG9 View 3D Structure Click here
A0A3P7E7H8 View 3D Structure Click here
A0A3P7GA09 View 3D Structure Click here
A0A5K4FBL2 View 3D Structure Click here
A4I1W6 View 3D Structure Click here
B4FXL2 View 3D Structure Click here
B8A1U0 View 3D Structure Click here
B9FDD2 View 3D Structure Click here
C0NT49 View 3D Structure Click here
C1H232 View 3D Structure Click here
C6SXT8 View 3D Structure Click here
K7LL37 View 3D Structure Click here
O43809 View 3D Structure Click here
Q0E8G6 View 3D Structure Click here
Q3ZCA2 View 3D Structure Click here
Q4CWE4 View 3D Structure Click here
Q4DVL1 View 3D Structure Click here
Q4KM65 View 3D Structure Click here
Q55E68 View 3D Structure Click here
Q57WN8 View 3D Structure Click here
Q5RAI8 View 3D Structure Click here
Q6ZIV4 View 3D Structure Click here
Q7T3C6 View 3D Structure Click here
Q8GXS3 View 3D Structure Click here
Q8I0V9 View 3D Structure Click here
Q8I712 View 3D Structure Click here
Q93716 View 3D Structure Click here
Q94AF0 View 3D Structure Click here
Q9CQF3 View 3D Structure Click here
U7Q4V0 View 3D Structure Click here