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5  structures 865  species 0  interactions 1934  sequences 82  architectures

Family: Collar (PF07484)

Summary: Phage Tail Collar Domain

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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 Tail Collar Domain Provide feedback

This region is occasionally found in conjunction with PF03335. Most of the family appear to be phage tail proteins; however some appear to be involved in other processes. For instance Q03314 from Rhizobium leguminosarum may be involved in plant-microbe interactions ([1]). A related protein Q9L3N1 is involved in the pathogenicity of Microcystis aeruginosa. The finding of this family in a structural component of the phage tail fibre baseplate (P10930) suggests that its function is structural rather than enzymatic. Structural studies show this region consists of a helix and a loop ([2]) and three beta-strands. This alignment does not catch the third strand as it is separated from the rest of the structure by around 100 residues. This strand is conserved in homologues but the intervening sequence is not. Much of the function of P10930 appears to reside in this intervening region. In the tertiary structure of the phage baseplate this domain forms part of the 'collar'. The domain may bind SO4, however the residues accredited with this vary between the PDB file and the Swiss-Prot entry. The long unconserved region maybe due to domain swapping in and out of a loop or reflective of rapid evolution.

Literature references

  1. Cubo MT, Economou A, Murphy G, Johnston AW, Downie JA; , J Bacteriol 1992;174:4026-4035.: Molecular characterization and regulation of the rhizosphere-expressed genes rhiABCR that can influence nodulation by Rhizobium leguminosarum biovar viciae. PUBMED:1597418 EPMC:1597418

  2. Thomassen E, Gielen G, Schutz M, Schoehn G, Abrahams JP, Miller S, van Raaij MJ; , J Mol Biol 2003;331:361-373.: The structure of the receptor-binding domain of the bacteriophage T4 short tail fibre reveals a knitted trimeric metal-binding fold. PUBMED:12888344 EPMC:12888344


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011083

This entry is represented by a domain found in Bacteriophage T4, Gp12. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

This region is occasionally found in conjunction with INTERPRO. Most of the proteins appear to be phage tail proteins; however some appear to be involved in other processes. For instance the RhiB protein (SWISSPROT) from Rhizobium leguminosarum may be involved in plant-microbe interactions [PUBMED:1597418]. A related protein, microcystin related protein (MrpB, SWISSPROT) is involved in the pathogenicity of Microcystis aeruginosa. The finding of this family in a structural component of the phage tail fibre baseplate (SWISSPROT) suggests that its function is structural rather than enzymatic. Structural studies show this region consists of a helix and a loop [PUBMED:12888344] and three beta-strands. This alignment does not catch the third strand as it is separated from the rest of the structure by around 100 residues. This strand is conserved in homologues but the intervening sequence is not. Much of the function of SWISSPROT appears to reside in this intervening region. In the tertiary structure of the phage baseplate this domain forms part of the collar and may bind SO4. The long unconserved region maybe due to domain swapping in and out of a loop or due to rapid evolution.

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
(181)
Full
(1934)
Representative proteomes NCBI
(1768)
Meta
(405)
RP15
(134)
RP35
(266)
RP55
(347)
RP75
(447)
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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
(181)
Full
(1934)
Representative proteomes NCBI
(1768)
Meta
(405)
RP15
(134)
RP35
(266)
RP55
(347)
RP75
(447)
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
(181)
Full
(1934)
Representative proteomes NCBI
(1768)
Meta
(405)
RP15
(134)
RP35
(266)
RP55
(347)
RP75
(447)
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: Yeats C
Previous IDs: none
Type: Domain
Author: Yeats C
Number in seed: 181
Number in full: 1934
Average length of the domain: 51.40 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 13.56 %

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 20.6 20.6
Trusted cut-off 20.6 20.6
Noise cut-off 20.5 20.5
Model length: 57
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 Collar domain has been found. There are 5 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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