Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
19  structures 18811  species 3  interactions 29852  sequences 26  architectures

Family: 5_3_exonuc (PF01367)

Summary: 5'-3' exonuclease, C-terminal SAM fold

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.

5'-3' exonuclease, C-terminal SAM fold Provide feedback

No Pfam abstract.

Literature references

  1. Eom SH, Wang J, Steitz TA; , Nature 1996;382:278-281.: Structure of Taq ploymerase with DNA at the polymerase active site. PUBMED:8717047 EPMC:8717047

  2. Ceska TA, Sayers JR, Stier G, Suck D; , Nature 1996;382:90-93.: A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease. PUBMED:8657312 EPMC:8657312

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR020045

This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include:

  • Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins [PUBMED:8674116].
  • 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [PUBMED:7637814, PUBMED:10666572].
  • Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases [PUBMED:9874768].
  • Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair [PUBMED:9699635].

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...

Loading domain graphics...

Pfam Clan

This family is a member of clan 5_3_exonuc_C (CL0464), which has the following description:

This superfamily includes C-terminal domains from a number of DNA-processing enzymes including T4 RNase H, 5' to 3' exonuclease domain of DNA polymerase Taq, T5 5'-exonuclease, Flap endonuclease-1 (Fen-1 nuclease), and other eukaryotic endonucleases.

The clan contains the following 4 members:

5_3_exonuc RNaseH_C XPG_I XPG_I_2


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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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.

Representative proteomes NCBI
Jalview View  View  View  View  View  View  View  View 
HTML View    View  View  View  View     
PP/heatmap 1   View  View  View  View     
Pfam viewer View  View             

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

Key: ✓ available, x not generated, not available.

Format an alignment

Representative proteomes NCBI

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.

Representative proteomes NCBI
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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_716 (release 3.0)
Previous IDs: 5_3_exonuclease;
Type: Domain
Author: Bateman A, Griffiths-Jones SR
Number in seed: 972
Number in full: 29852
Average length of the domain: 97.80 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 14.62 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 40.0 40.0
Trusted cut-off 40.0 40.0
Noise cut-off 39.8 39.9
Model length: 97
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

Sunburst controls


Weight segments by...

Change the size of the sunburst


Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls


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


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.


There are 3 interactions for this family. More...

5_3_exonuc_N DNA_pol_A 5_3_exonuc_N


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 5_3_exonuc domain has been found. There are 19 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 seqence.

Loading structure mapping...