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8  structures 262  species 0  interactions 357  sequences 4  architectures

Family: Phage_cap_P2 (PF05125)

Summary: Phage major capsid protein, P2 family

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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 major capsid protein, P2 family Provide feedback

No Pfam abstract.

Literature references

  1. Linderoth NA, Ziermann R, Haggard-Ljungquist E, Christie GE, Calendar R; , Nucleic Acids Res 1991;19:7207-7214.: Nucleotide sequence of the DNA packaging and capsid synthesis genes of bacteriophage P2. PUBMED:1837355 EPMC:1837355

This tab holds annotation information from the InterPro database.

InterPro entry IPR006441

This family represents the major capsid protein component of the heads (capsids) of bacteriophage P2 and related phage including prophage. These sequences represent one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease.

This entry is represented by Bacteriophage P2, GpN. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

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 Phage-coat (CL0373), which has the following description:

A number of different phage coat-proteins are collected together in this superfamily.

The clan contains the following 14 members:

DUF1884 DUF2184 DUF5309 DUF6260 Gp13-like Gp23 L_lactis_ph-MCP Linocin_M18 P22_CoatProtein PCLP Phage_cap_E Phage_cap_P2 Phage_capsid Phage_capsid_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 (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
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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
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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: TIGRFAMs (release 2.0);
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: TIGRFAMs, Finn RD
Number in seed: 28
Number in full: 357
Average length of the domain: 318.5 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 94.17 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.7 27.6
Noise cut-off 26.2 26.2
Model length: 327
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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


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


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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_cap_P2 domain has been found. There are 8 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
A0A0H3GKI8 View 3D Structure Click here
A0A0H3GTZ9 View 3D Structure Click here
A0A0H3GWD1 View 3D Structure Click here
Q8ZMT2 View 3D Structure Click here