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185  structures 8499  species 0  interactions 35613  sequences 449  architectures

Family: RNase_T (PF00929)

Summary: Exonuclease

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.

Exonuclease Provide feedback

This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;

Literature references

  1. Koonin EV, Deutscher MP; , Nucleic Acids Res 1993;21:2521-2522.: RNase T shares conserved sequence motifs with DNA proofreading exonucleases. PUBMED:8506149 EPMC:8506149


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013520

This entry includes a variety of exonuclease proteins, such as ribonuclease T [ PUBMED:8506149 ] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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
(40)
Full
(35613)
Representative proteomes UniProt
(141044)
RP15
(5226)
RP35
(16403)
RP55
(33945)
RP75
(57115)
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
(40)
Full
(35613)
Representative proteomes UniProt
(141044)
RP15
(5226)
RP35
(16403)
RP55
(33945)
RP75
(57115)
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
(40)
Full
(35613)
Representative proteomes UniProt
(141044)
RP15
(5226)
RP35
(16403)
RP55
(33945)
RP75
(57115)
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_1153 (release 3.0)
Previous IDs: Exonuclease; Exonuc_X-T;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 40
Number in full: 35613
Average length of the domain: 159.60 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 36.54 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 165
Family (HMM) version: 26
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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 RNase_T domain has been found. There are 185 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
A0A0G2KA38 View 3D Structure Click here
A0A0P0V145 View 3D Structure Click here
A0A0P0VNJ1 View 3D Structure Click here
A0A0P0WH57 View 3D Structure Click here
A0A0P0XTY0 View 3D Structure Click here
A0A0P0XUQ0 View 3D Structure Click here
A0A0P0Y2S5 View 3D Structure Click here
A0A0P0Y7W0 View 3D Structure Click here
A0A0R0EJ11 View 3D Structure Click here
A0A0R0FML0 View 3D Structure Click here
A0A0R0GCQ1 View 3D Structure Click here
A0A0R0H1D5 View 3D Structure Click here
A0A0R0ILP0 View 3D Structure Click here
A0A0R0K2D9 View 3D Structure Click here
A0A1D6DW13 View 3D Structure Click here
A0A1D6HHU9 View 3D Structure Click here
A0A1D6K822 View 3D Structure Click here
A0A1D6KQ53 View 3D Structure Click here
A0A1D6LIQ0 View 3D Structure Click here
A0A1D6LXY3 View 3D Structure Click here
A0A1D6MQY5 View 3D Structure Click here
A0A1D6MYG4 View 3D Structure Click here
A0A1D8PGG3 View 3D Structure Click here
A0A1P8BBT6 View 3D Structure Click here
A1A5R7 View 3D Structure Click here
A1Z7K9 View 3D Structure Click here
A3KH10 View 3D Structure Click here
A3KPE8 View 3D Structure Click here
A4HVE4 View 3D Structure Click here
A4I0S0 View 3D Structure Click here
A4I1I8 View 3D Structure Click here
A4I4A6 View 3D Structure Click here
A4I4A7 View 3D Structure Click here
A4I4A8 View 3D Structure Click here
A4I519 View 3D Structure Click here
A4I8A0 View 3D Structure Click here
A8K979 View 3D Structure Click here
B1WBN4 View 3D Structure Click here
B2GUW6 View 3D Structure Click here
B3LFC1 View 3D Structure Click here
B4FCU5 View 3D Structure Click here
B4FYY5 View 3D Structure Click here
B6U6C6 View 3D Structure Click here
B9FEC6 View 3D Structure Click here
C0P3D4 View 3D Structure Click here
C4J3C8 View 3D Structure Click here
C6THA2 View 3D Structure Click here
D4A3I6 View 3D Structure Click here
D4A625 View 3D Structure Click here
E7F5Q4 View 3D Structure Click here
E7FAN2 View 3D Structure Click here
E9QJN4 View 3D Structure Click here
F1QJP9 View 3D Structure Click here
F1QNX9 View 3D Structure Click here
F1R5B7 View 3D Structure Click here
F4JJ23 View 3D Structure Click here
I1JIS3 View 3D Structure Click here
I1JR73 View 3D Structure Click here
I1JZM8 View 3D Structure Click here
I1KDP8 View 3D Structure Click here
I1LB66 View 3D Structure Click here
I1LV41 View 3D Structure Click here
I1LXA9 View 3D Structure Click here
I1M0N0 View 3D Structure Click here
I1M796 View 3D Structure Click here
I1MCY4 View 3D Structure Click here
I1MIM2 View 3D Structure Click here
I1MTW0 View 3D Structure Click here
I1NBT2 View 3D Structure Click here
M0R8C5 View 3D Structure Click here
O16312 View 3D Structure Click here
O43414 View 3D Structure Click here
O44406 View 3D Structure Click here
O69678 View 3D Structure Click here
O94375 View 3D Structure Click here
O94443 View 3D Structure Click here
O94626 View 3D Structure Click here
P03007 View 3D Structure Click here
P04995 View 3D Structure Click here
P0A784 View 3D Structure Click here
P0AEK0 View 3D Structure Click here
P30014 View 3D Structure Click here
P53010 View 3D Structure Click here
P53015 View 3D Structure Click here
P53331 View 3D Structure Click here
P54964 View 3D Structure Click here
P9WIU1 View 3D Structure Click here
P9WLJ1 View 3D Structure Click here
Q08237 View 3D Structure Click here
Q08I43 View 3D Structure Click here
Q09798 View 3D Structure Click here
Q0J9I1 View 3D Structure Click here
Q0J9Z9 View 3D Structure Click here
Q0V842 View 3D Structure Click here
Q10905 View 3D Structure Click here
Q10MN9 View 3D Structure Click here
Q17819 View 3D Structure Click here
Q2FWZ6 View 3D Structure Click here
Q2FY88 View 3D Structure Click here
Q2FYH5 View 3D Structure Click here
Q2G1Z8 View 3D Structure Click here
Q3U1G5 View 3D Structure Click here
Q4CL08 View 3D Structure Click here
Q4CLD5 View 3D Structure Click here
Q4CVE6 View 3D Structure Click here
Q4D4F6 View 3D Structure Click here
Q4D4N5 View 3D Structure Click here
Q4D8C8 View 3D Structure Click here
Q4D8C9 View 3D Structure Click here
Q4D8D0 View 3D Structure Click here
Q4DFD2 View 3D Structure Click here
Q4DG67 View 3D Structure Click here
Q4DHR3 View 3D Structure Click here
Q4DIB7 View 3D Structure Click here
Q4DJ72 View 3D Structure Click here
Q4DQG3 View 3D Structure Click here
Q4DSW2 View 3D Structure Click here
Q4DV40 View 3D Structure Click here
Q4E271 View 3D Structure Click here
Q502M8 View 3D Structure Click here
Q503G0 View 3D Structure Click here
Q504Q3 View 3D Structure Click here
Q54RJ2 View 3D Structure Click here
Q54U94 View 3D Structure Click here
Q556Y2 View 3D Structure Click here
Q55DD5 View 3D Structure Click here
Q5A3Q0 View 3D Structure Click here
Q5A791 View 3D Structure Click here
Q5AAW5 View 3D Structure Click here
Q5APK0 View 3D Structure Click here
Q5BKS4 View 3D Structure Click here
Q5FVR4 View 3D Structure Click here
Q5U1X1 View 3D Structure Click here
Q5ZDI4 View 3D Structure Click here
Q682U6 View 3D Structure Click here
Q6AXU3 View 3D Structure Click here
Q6IE70 View 3D Structure Click here
Q6K4V8 View 3D Structure Click here
Q6PAQ4 View 3D Structure Click here
Q7F186 View 3D Structure Click here
Q7TMF2 View 3D Structure Click here
Q8BGF7 View 3D Structure Click here
Q8C460 View 3D Structure Click here
Q8IV48 View 3D Structure Click here
Q8L7M4 View 3D Structure Click here
Q8LAA0 View 3D Structure Click here
Q8W566 View 3D Structure Click here
Q8WTP8 View 3D Structure Click here
Q94285 View 3D Structure Click here
Q948H5 View 3D Structure Click here
Q95RQ4 View 3D Structure Click here
Q96AZ6 View 3D Structure Click here
Q96IC2 View 3D Structure Click here
Q9CA74 View 3D Structure Click here
Q9CZI9 View 3D Structure Click here
Q9D8S4 View 3D Structure Click here
Q9FFG1 View 3D Structure Click here
Q9FLR0 View 3D Structure Click here
Q9GZR2 View 3D Structure Click here
Q9H9L3 View 3D Structure Click here
Q9JL16 View 3D Structure Click here
Q9P7H2 View 3D Structure Click here
Q9R1A9 View 3D Structure Click here
Q9TZZ9 View 3D Structure Click here
Q9U220 View 3D Structure Click here
Q9VCI0 View 3D Structure Click here
Q9VRX7 View 3D Structure Click here
Q9VUC3 View 3D Structure Click here
Q9XXI3 View 3D Structure Click here
Q9Y3B8 View 3D Structure Click here
Q9ZU79 View 3D Structure Click here
Q9ZVE0 View 3D Structure Click here