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15  structures 13  species 0  interactions 100  sequences 3  architectures

Family: Pollen_allerg_2 (PF01620)

Summary: Ribonuclease (pollen allergen)

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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.

Ribonuclease (pollen allergen) Provide feedback

This family contains grass pollen proteins of group V. Q40963 has been shown to possess ribonuclease activity [1].

Literature references

  1. Bufe A, Schramm G, Keown MB, Schlaak M, Becker WM; , Febs lett 1995;363:6-12.: Major allergen Phl p Vb in timothy grass is a novel pollen RNase. PUBMED:7729555 EPMC:7729555


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002914

Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation.

The allergens in this family include allergens with the following designations: Lol p 5, Pha a 5, Phl p 5, Phl p 6, Phl p 11 and Poa p 9.

Grass pollen allergens are one of the major causes of type I allergies (including allergic rhinoconjunctivitis, allergic bronchial asthma and hayfever), afflicting 15-20% of a genetically predisposed population [PUBMED:1702432]. The predicted molecular masses of the known pollen allergen proteins range from 28.3 to 37.8kDa [PUBMED:1702432]. Northern analysis indicates that expression of the genes is confined to pollen tissue. A low level of similarity is observed between the Phl p 5 allergens and the N-terminal sequences of Poa pratensis (Kentucky bluegrass) p 9 proteins [PUBMED:2051020] (see INTERPRO).

The N-terminal region of P. pratensis p 9 has been shown to possess epitopes that cross-react with the acidic group V allergens of Phleum pratense (Common timothy) [PUBMED:2051020]. Comparison of amino acid sequences of recombinant P. pratensis p 9 proteins with those of Lol p 5 isoallergens revealed a low level of similarity between the N-terminal sequences of these proteins [PUBMED:2051020]. A C-terminal region (INTERPRO), conserved in P. pratensis p 9 allergens, appears to contain epitopes unique to these proteins [PUBMED:2051020].

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...

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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.

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(12)
Full
(100)
Representative proteomes NCBI
(117)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(2)
RP75
(2)
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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
(12)
Full
(100)
Representative proteomes NCBI
(117)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(2)
RP75
(2)
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
(12)
Full
(100)
Representative proteomes NCBI
(117)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(2)
RP75
(2)
Raw Stockholm Download   Download       Download   Download   Download    
Gzipped 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_1050 (release 4.1)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 12
Number in full: 100
Average length of the domain: 121.20 aa
Average identity of full alignment: 46 %
Average coverage of the sequence by the domain: 87.34 %

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 77.7 26.6
Noise cut-off 23.7 23.6
Model length: 156
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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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 Pollen_allerg_2 domain has been found. There are 15 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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