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.
22  structures 54  species 2  interactions 97  sequences 3  architectures

Family: T4_gp9_10 (PF07880)

Summary: Bacteriophage T4 gp9/10-like protein

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 T4 gp9/10-like protein Provide feedback

The members of this family are similar to gene products 9 (gp9) and 10 (gp10) of bacteriophage T4. Both proteins are components of the viral baseplate [1]. Gp9 (P10927) connects the long tail fibres of the virus to the baseplate and triggers tail contraction after viral attachment to a host cell. The protein is active as a trimer, with each monomer being composed of three domains. The N-terminal domain consists of an extended polypeptide chain and two alpha helices. The alpha1 helix from each of the three monomers in the trimer interacts with its counterparts to form a coiled-coil structure. The middle domain is a seven-stranded beta-sandwich that is thought to be a novel protein fold. The C-terminal domain is thought to be essential for gp9 trimerisation and is organised into an eight- stranded antiparallel beta-barrel, which was found to resemble the 'jelly roll' fold found in many viral capsid proteins. The long flexible region between the N-terminal and middle domains may be required for the function of gp9 to transmit signals from the long tail fibres [2]. Together with gp11, gp10 (P10928) initiates the assembly of wedges that then go on to associate with a hub to form the viral baseplate [1].

Literature references

  1. Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Ruger W; , Microbiol Mol Biol Rev 2003;67:86-156.: Bacteriophage T4 genome. PUBMED:12626685 EPMC:12626685

  2. Kostyuchenko VA, Navruzbekov GA, Kurochkina LP, Strelkov SV, Mesyanzhinov VV, Rossmann MG; , Structure Fold Des 1999;7:1213-1222.: The structure of bacteriophage T4 gene product 9: the trigger for tail contraction. PUBMED:10545330 EPMC:10545330


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008987

The Bacteriophage T4 is a double-stranded, structurally complex virus that infects Escherichia coli. Gene product 9 (gp9) connects the long tail fibres to the baseplate, and triggers baseplate reorganisation and tail contraction after virus attachment to the host cell. The gp9 protein forms a homotrimer, with each monomer having three domains: the N-terminal alpha-helical domain forms a triple coiled coil, the middle domain is a mixed, seven-stranded beta sandwich with a unique fold, and the C-terminal domain is a eight-stranded beta-sandwich with similarity to jellyroll viral capsid protein structures [PUBMED:10545330]. The flexible loops that occur between domains may enable the conformational changes necessary during infection.

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...

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
(14)
Full
(97)
Representative proteomes NCBI
(90)
Meta
(685)
RP15
(0)
RP35
(0)
RP55
(1)
RP75
(1)
Jalview View  View      View  View  View  View 
HTML View  View      View  View     
PP/heatmap 1 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
(14)
Full
(97)
Representative proteomes NCBI
(90)
Meta
(685)
RP15
(0)
RP35
(0)
RP55
(1)
RP75
(1)
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
(14)
Full
(97)
Representative proteomes NCBI
(90)
Meta
(685)
RP15
(0)
RP35
(0)
RP55
(1)
RP75
(1)
Raw Stockholm Download   Download       Download   Download   Download   Download  
Gzipped 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.

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_73396 (release 14.0)
Previous IDs: none
Type: Family
Author: Fenech M
Number in seed: 14
Number in full: 97
Average length of the domain: 229.60 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 52.13 %

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 25.0 25.0
Trusted cut-off 25.3 25.2
Noise cut-off 24.6 24.5
Model length: 278
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

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

Hide

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

Loading...

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.

Interactions

There are 2 interactions for this family. More...

T4_gp9_10 Phage-Gp8

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 T4_gp9_10 domain has been found. There are 22 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.

Loading structure mapping...