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0  structures 536  species 0  interactions 734  sequences 3  architectures

Family: Phage_GPO (PF05929)

Summary: Phage capsid scaffolding protein (GPO) serine peptidase

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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 capsid scaffolding protein (GPO) serine peptidase Provide feedback

This family consists of several bacteriophage capsid scaffolding proteins (GPO) and some related bacterial sequences. GPO is thought to function in both the assembly of proheads and the cleavage of GPN [1]. The family is found to function as a serine peptidase, with a conserved Asp, His and Ser catalytic triad, as in subtilisin, and as represented in S73. The family includes SwissProt:P25478 from Enterobacteria phage P2 which cleaves itself and then becomes the scaffold protein upon which the bacteriophage prohead is built - a mechanism quite common amongst phages [2].

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

  2. Chang JR, Spilman MS, Rodenburg CM, Dokland T; , 2008; [Epub ahead of print]: Functional domains of the bacteriophage P2 scaffolding protein: Identification of residues involved in assembly and protease activity. PUBMED:19064277 EPMC:19064277


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR009228

The bacteriophage P2 capsid is formed by multiple copies of the capsid protein GpN. The scaffolding protein GpO, which is essential for the assembly of this capsid, consists of an N-terminal serine protease domain and a C-terminal scaffolding domain [PUBMED:1837355, PUBMED:19064277]. During capsid assembly, GpO interacts with GpN via the N-terminal domain, while the C-terminal domain plays an essential role as a scaffold. When capsid assembly is complete the C-terminal domain of GpO is cleaved autocatalytically. Cleavage of GpN to its mature form by the remaining N-terminal domain then completes the maturation process.

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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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
(5)
Full
(734)
Representative proteomes NCBI
(566)
Meta
(6)
RP15
(10)
RP35
(33)
RP55
(56)
RP75
(77)
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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

  Seed
(5)
Full
(734)
Representative proteomes NCBI
(566)
Meta
(6)
RP15
(10)
RP35
(33)
RP55
(56)
RP75
(77)
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
(5)
Full
(734)
Representative proteomes NCBI
(566)
Meta
(6)
RP15
(10)
RP35
(33)
RP55
(56)
RP75
(77)
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: Pfam-B_1730 (release 9.0)
Previous IDs: none
Type: Family
Author: Moxon SJ
Number in seed: 5
Number in full: 734
Average length of the domain: 255.80 aa
Average identity of full alignment: 42 %
Average coverage of the sequence by the domain: 93.46 %

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 21.5 21.5
Trusted cut-off 22.8 22.5
Noise cut-off 21.4 21.4
Model length: 276
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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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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