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.
0  structures 305  species 0  interactions 432  sequences 7  architectures

Family: Phage_GPA (PF05840)

Summary: Bacteriophage replication gene A protein (GPA)

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.

Bacteriophage replication gene A protein (GPA) Provide feedback

This family consists of a group of bacteriophage replication gene A protein (GPA) like sequences from both viruses and bacteria. The members of this family are likely to be endonucleases [1,2,3].

Literature references

  1. Liu Y, Saha S, Haggard-Ljungquist E; , J Mol Biol 1993;231:361-374.: Studies of bacteriophage P2 DNA replication. The DNA sequence of the cis-acting gene A and ori region and construction of a P2 mini-chromosome. PUBMED:8510152 EPMC:8510152

  2. Esposito D, Scocca JJ; , Mol Microbiol 1994;13:685-695.: Identification of an HP1 phage protein required for site-specific excision. PUBMED:7997180 EPMC:7997180

  3. Hsu MY, Inouye M, Inouye S; , Proc Natl Acad Sci U S A 1990;87:9454-9458.: Retron for the 67-base multicopy single-stranded DNA from Escherichia coli: a potential transposable element encoding both reverse transcriptase and Dam methylase functions. PUBMED:1701261 EPMC:1701261

  4. Ikeda JE, Yudelevich A, Shimamoto N, Hurwitz J; , J Biol Chem 1979;254:9416-9428.: Role of polymeric forms of the bacteriophage phi X174 coded gene A protein in phi XRFI DNA cleavage. PUBMED:158588 EPMC:158588

  5. van Mansfeld AD, van Teeffelen HA, Baas PD, Jansz HS; , Nucleic Acids Res 1986;14:4229-4238.: Two juxtaposed tyrosyl-OH groups participate in phi X174 gene A protein catalysed cleavage and ligation of DNA. PUBMED:2940511 EPMC:2940511

This tab holds annotation information from the InterPro database.

InterPro entry IPR008766

Replication gene A proteins (also known as GpA) are found in bacteriophages and in bacteria as part of a suspected prophage. These proteins function as endonucleases during DNA replication [ PUBMED:8510152 , PUBMED:7997180 , PUBMED:1701261 ].

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 Rep (CL0169), which has the following description:

This clan includes replication proteins for viruses and plasmids. This domain is known to bind DNA. The members of this clan have three motifs. The central HXH is conserved in most families in the clan.

The clan contains the following 14 members:

DUF1424 Gemini_AL1 Mob_Pre MobA_MobL MobL Phage_GPA PV_NSP1 Relaxase Rep_1 Rep_2 Rep_N T_Ag_DNA_bind TrwC Viral_Rep


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.

Representative proteomes UniProt
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

Representative proteomes UniProt

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 UniProt
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...


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_8738 (release 8.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Moxon SJ
Number in seed: 11
Number in full: 432
Average length of the domain: 284.30 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 47.52 %

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 31.4 31.4
Trusted cut-off 31.9 31.7
Noise cut-off 30.9 30.8
Model length: 318
Family (HMM) version: 15
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.

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;