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0  structures 3244  species 0  interactions 4701  sequences 6  architectures

Family: Phage_tube (PF04985)

Summary: Phage tail tube protein FII

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Phage tail tube protein FII Provide feedback

The major structural components of the contractile tail of bacteriophage P2 are proteins FI and FII, which are believed to be the tail sheath and tube proteins, respectively.

Literature references

  1. Temple LM, Forsburg SL, Calendar R, Christie GE; , Virology 1991;181:353-358.: Nucleotide sequence of the genes encoding the major tail sheath and tail tube proteins of bacteriophage P2. PUBMED:1825255 EPMC:1825255

  2. Xue Q, Egan JB; , Virology 1995;212:218-221.: Tail sheath and tail tube genes of the temperate coliphage 186. PUBMED:7676633 EPMC:7676633

  3. Pell LG, Cumby N, Clark TE, Tuite A, Battaile KP, Edwards AM, Chirgadze NY, Davidson AR, Maxwell KL;, J Mol Biol. 2013;425:2436-2449.: A conserved spiral structure for highly diverged phage tail assembly chaperones. PUBMED:23542344 EPMC:23542344


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006498

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

The tails of some phage are contractile. These sequences represent the tail tube, or tail core, protein of the contractile tail of phage P2, and homologous proteins from other phage.

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_TTPs (CL0569), which has the following description:

This superfamily represents families of phage tail tube proteins TTPs. Most bacteriophages possess a long tail that is either non-contractile as in the Siphoviridae family or contractile as in the Myoviridae family. These multi-component structures are assembled in regulated pathways that commence with the formation of the tail tip. Tail tip complexes, also referred to as baseplates in some phages, vary considerably in size and protein composition, but all probably serve as the initiator of tail tube protein polymerisation. The tube protein in each case is a long tubular strucutre through which the viral DNA passes during infection. The tube is created by polymerisation of the tube single tube protein. Contractile tails include a central tail tube protein (TTP) that is surrounded by a tail sheath protein (TSP). On infection, the tail sheath contracts and the TTP penetrates the outer cell membrane and cell wall [1,2,3].

The clan contains the following 9 members:

L_lac_phage_MSP Phage_T4_gp19 Phage_tail_2 Phage_tail_3 Phage_TTP_1 Phage_TTP_11 Phage_TTP_12 Phage_TTP_13 Phage_tube

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...

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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
(106)
Full
(4701)
Representative proteomes NCBI
(1639)
Meta
(22)
RP15
(28)
RP35
(81)
RP55
(140)
RP75
(217)
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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
(106)
Full
(4701)
Representative proteomes NCBI
(1639)
Meta
(22)
RP15
(28)
RP35
(81)
RP55
(140)
RP75
(217)
Alignment:
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Sequence:
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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
(106)
Full
(4701)
Representative proteomes NCBI
(1639)
Meta
(22)
RP15
(28)
RP35
(81)
RP55
(140)
RP75
(217)
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.

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: COG3498
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 106
Number in full: 4701
Average length of the domain: 163.70 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 96.89 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.4 22.4
Trusted cut-off 22.7 24.2
Noise cut-off 21.9 21.4
Model length: 166
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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