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13  structures 4035  species 1  interaction 10422  sequences 29  architectures

Family: Phage_int_SAM_1 (PF02899)

Summary: Phage integrase, N-terminal SAM-like domain

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, N-terminal SAM-like domain Provide feedback

No Pfam abstract.

Literature references

  1. Subramanya HS, Arciszewska LK, Baker RA, Bird LE, Sherratt DJ, Wigley DB; , EMBO J 1997;16:5178-5187.: Crystal structure of the site-specific recombinase, XerD. PUBMED:9311978 EPMC:9311978


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004107

Proteins containing this domain 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 phage integrase N-terminal SAM-like domain is almost always found with the signature that defines the phage integrase family (see INTERPRO).

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 l-integrase_N (CL0469), which has the following description:

This superfamily is characterised by families having 4-5 helices in a bundle of two orthogonally packed alpha-hairpins that are involved in interactions with DNA and proteins.

The clan contains the following 5 members:

Phage_int_SAM_1 Phage_int_SAM_2 Phage_int_SAM_3 Phage_int_SAM_4 Phage_int_SAM_5

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 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.

  Seed
(37)
Full
(10422)
Representative proteomes NCBI
(8796)
Meta
(3027)
RP15
(747)
RP35
(1479)
RP55
(1975)
RP75
(2334)
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

  Seed
(37)
Full
(10422)
Representative proteomes NCBI
(8796)
Meta
(3027)
RP15
(747)
RP35
(1479)
RP55
(1975)
RP75
(2334)
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
(37)
Full
(10422)
Representative proteomes NCBI
(8796)
Meta
(3027)
RP15
(747)
RP35
(1479)
RP55
(1975)
RP75
(2334)
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.

Pfam alignments:

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: Structural domain
Previous IDs: Phage_integr_N;
Type: Domain
Author: Griffiths-Jones SR
Number in seed: 37
Number in full: 10422
Average length of the domain: 83.20 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 26.81 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.2 21.2
Trusted cut-off 21.2 21.2
Noise cut-off 21.1 21.1
Model length: 84
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

Sunburst controls

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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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Tree controls

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

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Interactions

There is 1 interaction for this family. More...

Phage_integrase

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_int_SAM_1 domain has been found. There are 13 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.

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