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.
118  structures 8379  species 0  interactions 67609  sequences 264  architectures

Family: Phage_integrase (PF00589)

Summary: Phage integrase family

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.

Phage integrase family Provide feedback

Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase (P06956) are Arg-173, His-289, Arg-292 and Tyr-324.

Literature references

  1. Kwon HJ, Tirumalai R, Landy A, Ellenberger T; , Science 1997;276:126-131.: Flexibility in DNA recombination: structure of the lambda integrase catalytic core. PUBMED:9082984 EPMC:9082984

  2. Guo F, Gopaul DN, van Duyne GD; , Nature 1997;389:40-46.: Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. PUBMED:9288963 EPMC:9288963


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002104

Phage integrase proteins cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [ PUBMED:9082984 , PUBMED:9288963 ].

The catalytic site residues in CRE recombinase ( SWISSPROT ) are Arg-173, His-289, Arg-292 and Tyr-324.

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 DNA-mend (CL0382), which has the following description:

This is a superfamily of DNA recombinases, topoisomerases and integrases.

The clan contains the following 10 members:

DUF3435 DUF3504 Flp_C Integrase_1 NDC10_II Phage_Integr_2 Phage_integr_3 Phage_integrase Telomere_res Topoisom_I

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
(24)
Full
(67609)
Representative proteomes UniProt
(368276)
RP15
(9390)
RP35
(32728)
RP55
(69536)
RP75
(124444)
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
(24)
Full
(67609)
Representative proteomes UniProt
(368276)
RP15
(9390)
RP35
(32728)
RP55
(69536)
RP75
(124444)
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
(24)
Full
(67609)
Representative proteomes UniProt
(368276)
RP15
(9390)
RP35
(32728)
RP55
(69536)
RP75
(124444)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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: MRC-LMB Genome group
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 24
Number in full: 67609
Average length of the domain: 169.90 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 49.37 %

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 27.1 27.1
Trusted cut-off 27.1 27.1
Noise cut-off 27.0 27.0
Model length: 172
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

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

Hide

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

Loading...

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 Phage_integrase domain has been found. There are 118 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.

Loading structure mapping...

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
C0H5A8 View 3D Structure Click here
I6XEU5 View 3D Structure Click here
O69718 View 3D Structure Click here
P0A8P6 View 3D Structure Click here
P0A8P8 View 3D Structure Click here
P0ADH5 View 3D Structure Click here
P0ADH7 View 3D Structure Click here
P24218 View 3D Structure Click here
P32053 View 3D Structure Click here
P37326 View 3D Structure Click here
P39347 View 3D Structure Click here
P71298 View 3D Structure Click here
P71903 View 3D Structure Click here
P75969 View 3D Structure Click here
P76056 View 3D Structure Click here
P76168 View 3D Structure Click here
P76542 View 3D Structure Click here
P9WF33 View 3D Structure Click here
P9WF35 View 3D Structure Click here
P9WMB3 View 3D Structure Click here
Q2FWP2 View 3D Structure Click here
Q2FX17 View 3D Structure Click here
Q2FY74 View 3D Structure Click here
Q2FY83 View 3D Structure Click here
Q2FZ30 View 3D Structure Click here
Q2G109 View 3D Structure Click here
Q2G2V0 View 3D Structure Click here
Q54AN0 View 3D Structure Click here
Q54AP1 View 3D Structure Click here
Q54AQ6 View 3D Structure Click here
Q54YI8 View 3D Structure Click here
Q55GY6 View 3D Structure Click here
Q55GZ4 View 3D Structure Click here
Q55GZ6 View 3D Structure Click here
Q55H10 View 3D Structure Click here
Q55H27 View 3D Structure Click here
Q55H32 View 3D Structure Click here
Q55H37 View 3D Structure Click here
Q55H39 View 3D Structure Click here
Q55H48 View 3D Structure Click here
Q55H58 View 3D Structure Click here
Q55H60 View 3D Structure Click here
Q57813 View 3D Structure Click here
Q58180 View 3D Structure Click here