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3  structures 1991  species 0  interactions 3192  sequences 9  architectures

Family: Phage_portal (PF04860)

Summary: Phage portal protein

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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 portal protein Provide feedback

Bacteriophage portal proteins form a dodecamer and is located at a five-fold vertex of the viral capsid. The portal complex forms a channel through which the viral DNA is packaged into the capsid, and exits during infection. The portal protein is though to rotate during DNA packaging [1]. Portal proteins from different phage show little sequence homology, so this family does not represent all portal proteins.

Literature references

  1. Moore SD, Prevelige PE Jr; , Curr Biol 2002;12:96-98.: DNA packaging: a new class of molecular motors. PUBMED:11839289 EPMC:11839289


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006944

This is a family of bacteriophage, prophage and Gene Transfer Agent (GTA) portal proteins. Positioned at one of the twelve icosahedral vertices, of the viral capsid, is a dodecameric complex of the virus encoded portal protein. This dodecameric complex, known as the portal or connector complex, forms the channel through which the viral DNA is packaged into the capsid, and through which it exits during infection. While the portal proteins from different phage show relatively little sequence homology and vary widely in molecular weight, portal complexes display significant morphological similarity as determined by electron microscopy. Morphologically, they present as disk-like structures approximately 150 Angstroms in diameter with radially arranged projections and a 30 Angstroms central channel. The packaging reaction is energy dependent and typically involves several components. ATP hydrolysis provides the driving force, and it is estimated that one ATP molecule is required for every base pair that is packaged. It appears that the portal motor may represent a new and extremely powerful class of motor which couples rotation to DNA translocation [PUBMED:11839289].

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
(127)
Full
(3192)
Representative proteomes NCBI
(2728)
Meta
(646)
RP15
(123)
RP35
(284)
RP55
(381)
RP75
(469)
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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
(127)
Full
(3192)
Representative proteomes NCBI
(2728)
Meta
(646)
RP15
(123)
RP35
(284)
RP55
(381)
RP75
(469)
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
(127)
Full
(3192)
Representative proteomes NCBI
(2728)
Meta
(646)
RP15
(123)
RP35
(284)
RP55
(381)
RP75
(469)
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_6050 (release 7.6)
Previous IDs: none
Type: Family
Author: Kerrison ND
Number in seed: 127
Number in full: 3192
Average length of the domain: 315.20 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 80.95 %

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 27.9 27.9
Trusted cut-off 27.9 28.2
Noise cut-off 27.7 27.8
Model length: 347
Family (HMM) version: 7
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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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_portal domain has been found. There are 3 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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